repo_name stringlengths 6 101 | path stringlengths 4 300 | text stringlengths 7 1.31M |
|---|---|---|
leafiy/miniblog | website/vue.config.js | const path = require('path')
const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin
const HTMLWebpackPlugin = require('html-webpack-plugin')
const webpack = require('webpack')
module.exports = {
devServer: {
open: false,
port: 8040,
https: false,
hotOnly: false,
bonjour: true,
allowedHosts: ['qiansmile.local'],
proxy: null, // string | Object
before: app => {
// app is an express instance
}
},
productionSourceMap: false,
configureWebpack: config => {
return {
entry: {
'mavon-editor': ['mavon-editor']
}
}
}
} |
voxel-web/samson | test/controllers/versions_controller_test.rb | <gh_stars>1-10
# frozen_string_literal: true
require_relative '../test_helper'
SingleCov.covered!
describe VersionsController do
def create_version(user)
PaperTrail.with_whodunnit_user(user) do
PaperTrail.with_logging do
stage.update_attribute(:name, 'Fooo')
end
end
end
let(:stage) { stages(:test_staging) }
as_a_viewer do
describe "#index" do
before { create_version user }
it "renders" do
get :index, params: {item_id: stage.id, item_type: stage.class.name}
assert_template :index
end
it "renders with jenkins job name" do
stage.update_attribute(:jenkins_job_names, 'jenkins-job-1')
stage.update_attribute(:jenkins_job_names, 'jenkins-job-2')
get :index, params: {item_id: stage.id, item_type: stage.class.name}
assert_template :index
assert_select 'p', text: /jenkins-job-1/
end
it "renders with unfound user" do
create_version(User.new { |u| u.id = 1211212 })
get :index, params: {item_id: stage.id, item_type: stage.class.name}
assert_template :index
end
it "renders with deleted item" do
stage.delete
get :index, params: {item_id: stage.id, item_type: stage.class.name}
assert_template :index
end
it "renders with removed class" do
stage.versions.last.update_column(:item_type, 'Whooops')
get :index, params: {item_id: stage.id, item_type: 'Whooops'}
assert_template :index
end
end
end
end
|
Amin-MAG/CodART | benchmark_projects/ganttproject/ganttproject/src/main/java/net/sourceforge/ganttproject/action/task/IndentTargetFunctionFactory.java | /*
Copyright 2012 GanttProject Team
This file is part of GanttProject, an opensource project management tool.
GanttProject is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
GanttProject is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with GanttProject. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.ganttproject.action.task;
import java.util.Collection;
import net.sourceforge.ganttproject.task.Task;
import net.sourceforge.ganttproject.task.TaskContainmentHierarchyFacade;
import net.sourceforge.ganttproject.task.TaskManager;
import com.google.common.base.Function;
/**
* Creates functions resolving move target for indent operations. Function depends on the set of tasks being moved so
* it is different every time
*
* @author dbarashev
*/
class IndentTargetFunctionFactory implements Function<Collection<Task>, Function<Task, Task>> {
private final TaskManager myTaskManager;
IndentTargetFunctionFactory(TaskManager taskManager) {
myTaskManager = taskManager;
}
@Override
public Function<Task, Task> apply(final Collection<Task> indentRoots) {
return new Function<Task, Task>() {
private final TaskContainmentHierarchyFacade myTaskHierarchy = myTaskManager.getTaskHierarchy();
@Override
public Task apply(Task whatMove) {
Task moveTarget = whatMove;
for (; moveTarget != null && indentRoots.contains(moveTarget);
moveTarget = myTaskHierarchy.getPreviousSibling(moveTarget));
return moveTarget;
}
};
}
}; |
Kamahl19/dokina | src/index.js | <gh_stars>0
import { AppRegistry, Platform } from 'react-native';
import KeyboardManager from 'react-native-keyboard-manager';
import Root from './app/containers/Root';
AppRegistry.registerComponent('dokina', () => Root);
if (Platform.OS === 'ios') {
KeyboardManager.setEnable(true);
KeyboardManager.setEnableAutoToolbar(false);
}
|
bryan-brancotte/rank-aggregation-with-ties | sources/rnt/mediane/algorithms/lri/ExactAlgorithm_preprocessing.py | from mediane.algorithms.lri.CondorcetPartitiong import CondorcetPartitioning
from mediane.algorithms.lri.ExactAlgorithm_bis import ExactAlgorithmBis
class ExactAlgorithmPreprocessing(CondorcetPartitioning):
def __init__(self):
super().__init__(ExactAlgorithmBis())
def get_full_name(self):
return "ExactAlgorithm_preprocessing"
def can_be_executed(self) -> bool:
return ExactAlgorithmBis().can_be_executed() and CondorcetPartitioning().can_be_executed()
|
coolgeeck/delwar1 | azure_functions_devops_build/service_endpoint/github_service_endpoint_manager.py | import vsts.service_endpoint.v4_1.models as models
from vsts.exceptions import VstsServiceError
from ..base.base_manager import BaseManager
from .service_endpoint_utils import sanitize_github_repository_fullname
class GithubServiceEndpointManager(BaseManager):
def __init__(self, organization_name, project_name, creds):
super(GithubServiceEndpointManager, self).__init__(
creds, organization_name=organization_name, project_name=project_name
)
def get_github_service_endpoints(self, repository_fullname):
service_endpoint_name = self._get_service_github_endpoint_name(repository_fullname)
try:
result = self._service_endpoint_client.get_service_endpoints_by_names(
self._project_name,
[service_endpoint_name],
type="github"
)
except VstsServiceError:
return []
return result
def create_github_service_endpoint(self, repository_fullname, github_pat):
data = {}
auth = models.endpoint_authorization.EndpointAuthorization(
parameters={
"accessToken": github_pat
},
scheme="PersonalAccessToken"
)
service_endpoint_name = self._get_service_github_endpoint_name(repository_fullname)
service_endpoint = models.service_endpoint.ServiceEndpoint(
administrators_group=None,
authorization=auth,
data=data,
name=service_endpoint_name,
type="github",
url="http://github.com"
)
return self._service_endpoint_client.create_service_endpoint(service_endpoint, self._project_name)
def _get_service_github_endpoint_name(self, repository_name):
return sanitize_github_repository_fullname(repository_name)
|
wanton-wind/M-compiler | idea/src/Compiler2018/Parser/MParser.java | // Generated from D:/Coding/M-compiler/idea/src/Compiler2018\M.g4 by ANTLR 4.7
package Compiler2018.Parser;
import org.antlr.v4.runtime.*;
import org.antlr.v4.runtime.atn.ATN;
import org.antlr.v4.runtime.atn.ATNDeserializer;
import org.antlr.v4.runtime.atn.ParserATNSimulator;
import org.antlr.v4.runtime.atn.PredictionContextCache;
import org.antlr.v4.runtime.dfa.DFA;
import org.antlr.v4.runtime.tree.ParseTreeListener;
import org.antlr.v4.runtime.tree.TerminalNode;
import java.util.List;
@SuppressWarnings({"all", "warnings", "unchecked", "unused", "cast"})
public class MParser extends Parser {
static {
RuntimeMetaData.checkVersion("4.7", RuntimeMetaData.VERSION);
}
protected static final DFA[] _decisionToDFA;
protected static final PredictionContextCache _sharedContextCache = new PredictionContextCache();
public static final int Bool = 1,
Int = 2,
String = 3,
Void = 4,
If = 5,
Else = 6,
For = 7,
While = 8,
Break = 9,
Continue = 10,
Return = 11,
New = 12,
Class = 13,
Add = 14,
Sub = 15,
Mul = 16,
Div = 17,
Mod = 18,
LT = 19,
GT = 20,
LE = 21,
GE = 22,
EQ = 23,
NE = 24,
And = 25,
Or = 26,
Not = 27,
LShift = 28,
RShift = 29,
BNot = 30,
BOr = 31,
BXor = 32,
BAnd = 33,
Assign = 34,
AddAdd = 35,
SubSub = 36,
Semi = 37,
Comma = 38,
Dot = 39,
LParen = 40,
RParen = 41,
LBracket = 42,
RBracket = 43,
LBrace = 44,
RBrace = 45,
BoolConst = 46,
NumConst = 47,
StrConst = 48,
NullConst = 49,
Identifier = 50,
WhiteSpace = 51,
LineComment = 52,
BlockComment = 53;
public static final int RULE_program = 0,
RULE_programSection = 1,
RULE_classDeclaration = 2,
RULE_functionDeclaration = 3,
RULE_variableDeclaration = 4,
RULE_variableDeclarationStatement = 5,
RULE_functionParameters = 6,
RULE_classBlock = 7,
RULE_classBlockItem = 8,
RULE_constructorDeclaration = 9,
RULE_statement = 10,
RULE_blockStatement = 11,
RULE_branchStatement = 12,
RULE_loopStatement = 13,
RULE_jumpStatement = 14,
RULE_classType = 15,
RULE_arrayClass = 16,
RULE_nonArrayClass = 17,
RULE_expression = 18,
RULE_callParameter = 19,
RULE_newObject = 20,
RULE_brackets = 21,
RULE_constant = 22;
public static final String[] ruleNames = {
"program",
"programSection",
"classDeclaration",
"functionDeclaration",
"variableDeclaration",
"variableDeclarationStatement",
"functionParameters",
"classBlock",
"classBlockItem",
"constructorDeclaration",
"statement",
"blockStatement",
"branchStatement",
"loopStatement",
"jumpStatement",
"classType",
"arrayClass",
"nonArrayClass",
"expression",
"callParameter",
"newObject",
"brackets",
"constant"
};
private static final String[] _LITERAL_NAMES = {
null,
"'bool'",
"'int'",
"'string'",
"'void'",
"'if'",
"'else'",
"'for'",
"'while'",
"'break'",
"'continue'",
"'return'",
"'new'",
"'class'",
"'+'",
"'-'",
"'*'",
"'/'",
"'%'",
"'<'",
"'>'",
"'<='",
"'>='",
"'=='",
"'!='",
"'&&'",
"'||'",
"'!'",
"'<<'",
"'>>'",
"'~'",
"'|'",
"'^'",
"'&'",
"'='",
"'++'",
"'--'",
"';'",
"','",
"'.'",
"'('",
"')'",
"'['",
"']'",
"'{'",
"'}'",
null,
null,
null,
"'null'"
};
private static final String[] _SYMBOLIC_NAMES = {
null,
"Bool",
"Int",
"String",
"Void",
"If",
"Else",
"For",
"While",
"Break",
"Continue",
"Return",
"New",
"IRClass",
"Add",
"Sub",
"Mul",
"Div",
"Mod",
"LT",
"GT",
"LE",
"GE",
"EQ",
"NE",
"And",
"Or",
"Not",
"LShift",
"RShift",
"BNot",
"BOr",
"BXor",
"BAnd",
"Assign",
"AddAdd",
"SubSub",
"Semi",
"Comma",
"Dot",
"LParen",
"RParen",
"LBracket",
"RBracket",
"LBrace",
"RBrace",
"BoolConst",
"NumConst",
"StrConst",
"NullConst",
"Identifier",
"WhiteSpace",
"LineComment",
"BlockComment"
};
public static final Vocabulary VOCABULARY = new VocabularyImpl(_LITERAL_NAMES, _SYMBOLIC_NAMES);
/**
* @deprecated Use {@link #VOCABULARY} instead.
*/
@Deprecated
public static final String[] tokenNames;
static {
tokenNames = new String[_SYMBOLIC_NAMES.length];
for (int i = 0; i < tokenNames.length; i++) {
tokenNames[i] = VOCABULARY.getLiteralName(i);
if (tokenNames[i] == null) {
tokenNames[i] = VOCABULARY.getSymbolicName(i);
}
if (tokenNames[i] == null) {
tokenNames[i] = "<INVALID>";
}
}
}
@Override
@Deprecated
public String[] getTokenNames() {
return tokenNames;
}
@Override
public Vocabulary getVocabulary() {
return VOCABULARY;
}
@Override
public String getGrammarFileName() {
return "M.g4";
}
@Override
public String[] getRuleNames() {
return ruleNames;
}
@Override
public String getSerializedATN() {
return _serializedATN;
}
@Override
public ATN getATN() {
return _ATN;
}
public MParser(TokenStream input) {
super(input);
_interp = new ParserATNSimulator(this, _ATN, _decisionToDFA, _sharedContextCache);
}
public static class ProgramContext extends ParserRuleContext {
public TerminalNode EOF() {
return getToken(MParser.EOF, 0);
}
public List<ProgramSectionContext> programSection() {
return getRuleContexts(ProgramSectionContext.class);
}
public ProgramSectionContext programSection(int i) {
return getRuleContext(ProgramSectionContext.class, i);
}
public ProgramContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_program;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterProgram(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitProgram(this);
}
}
public final ProgramContext program() throws RecognitionException {
ProgramContext _localctx = new ProgramContext(_ctx, getState());
enterRule(_localctx, 0, RULE_program);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(49);
_errHandler.sync(this);
_la = _input.LA(1);
while ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << Bool)
| (1L << Int)
| (1L << String)
| (1L << Void)
| (1L << Class)
| (1L << Identifier)))
!= 0)) {
{
{
setState(46);
programSection();
}
}
setState(51);
_errHandler.sync(this);
_la = _input.LA(1);
}
setState(52);
match(EOF);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ProgramSectionContext extends ParserRuleContext {
public ProgramSectionContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_programSection;
}
public ProgramSectionContext() {
}
public void copyFrom(ProgramSectionContext ctx) {
super.copyFrom(ctx);
}
}
public static class ClassDeclContext extends ProgramSectionContext {
public ClassDeclarationContext classDeclaration() {
return getRuleContext(ClassDeclarationContext.class, 0);
}
public ClassDeclContext(ProgramSectionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterClassDecl(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitClassDecl(this);
}
}
public static class VarDeclContext extends ProgramSectionContext {
public VariableDeclarationStatementContext variableDeclarationStatement() {
return getRuleContext(VariableDeclarationStatementContext.class, 0);
}
public VarDeclContext(ProgramSectionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterVarDecl(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitVarDecl(this);
}
}
public static class FuncDeclContext extends ProgramSectionContext {
public FunctionDeclarationContext functionDeclaration() {
return getRuleContext(FunctionDeclarationContext.class, 0);
}
public FuncDeclContext(ProgramSectionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterFuncDecl(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitFuncDecl(this);
}
}
public final ProgramSectionContext programSection() throws RecognitionException {
ProgramSectionContext _localctx = new ProgramSectionContext(_ctx, getState());
enterRule(_localctx, 2, RULE_programSection);
try {
setState(57);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 1, _ctx)) {
case 1:
_localctx = new ClassDeclContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(54);
classDeclaration();
}
break;
case 2:
_localctx = new FuncDeclContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(55);
functionDeclaration();
}
break;
case 3:
_localctx = new VarDeclContext(_localctx);
enterOuterAlt(_localctx, 3);
{
setState(56);
variableDeclarationStatement();
}
break;
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ClassDeclarationContext extends ParserRuleContext {
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public ClassBlockContext classBlock() {
return getRuleContext(ClassBlockContext.class, 0);
}
public ClassDeclarationContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_classDeclaration;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterClassDeclaration(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitClassDeclaration(this);
}
}
public final ClassDeclarationContext classDeclaration() throws RecognitionException {
ClassDeclarationContext _localctx = new ClassDeclarationContext(_ctx, getState());
enterRule(_localctx, 4, RULE_classDeclaration);
try {
enterOuterAlt(_localctx, 1);
{
setState(59);
match(Class);
setState(60);
match(Identifier);
setState(61);
classBlock();
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class FunctionDeclarationContext extends ParserRuleContext {
public ClassTypeContext classType() {
return getRuleContext(ClassTypeContext.class, 0);
}
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public BlockStatementContext blockStatement() {
return getRuleContext(BlockStatementContext.class, 0);
}
public FunctionParametersContext functionParameters() {
return getRuleContext(FunctionParametersContext.class, 0);
}
public FunctionDeclarationContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_functionDeclaration;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterFunctionDeclaration(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitFunctionDeclaration(this);
}
}
public final FunctionDeclarationContext functionDeclaration() throws RecognitionException {
FunctionDeclarationContext _localctx = new FunctionDeclarationContext(_ctx, getState());
enterRule(_localctx, 6, RULE_functionDeclaration);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(63);
classType();
setState(64);
match(Identifier);
setState(65);
match(LParen);
setState(67);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << Bool)
| (1L << Int)
| (1L << String)
| (1L << Void)
| (1L << Identifier)))
!= 0)) {
{
setState(66);
functionParameters();
}
}
setState(69);
match(RParen);
setState(70);
blockStatement();
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class VariableDeclarationContext extends ParserRuleContext {
public ClassTypeContext classType() {
return getRuleContext(ClassTypeContext.class, 0);
}
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public VariableDeclarationContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_variableDeclaration;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterVariableDeclaration(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitVariableDeclaration(this);
}
}
public final VariableDeclarationContext variableDeclaration() throws RecognitionException {
VariableDeclarationContext _localctx = new VariableDeclarationContext(_ctx, getState());
enterRule(_localctx, 8, RULE_variableDeclaration);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(72);
classType();
setState(73);
match(Identifier);
setState(76);
_errHandler.sync(this);
_la = _input.LA(1);
if (_la == Assign) {
{
setState(74);
match(Assign);
setState(75);
expression(0);
}
}
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class VariableDeclarationStatementContext extends ParserRuleContext {
public VariableDeclarationContext variableDeclaration() {
return getRuleContext(VariableDeclarationContext.class, 0);
}
public VariableDeclarationStatementContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_variableDeclarationStatement;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener)
((MListener) listener).enterVariableDeclarationStatement(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener)
((MListener) listener).exitVariableDeclarationStatement(this);
}
}
public final VariableDeclarationStatementContext variableDeclarationStatement()
throws RecognitionException {
VariableDeclarationStatementContext _localctx =
new VariableDeclarationStatementContext(_ctx, getState());
enterRule(_localctx, 10, RULE_variableDeclarationStatement);
try {
enterOuterAlt(_localctx, 1);
{
setState(78);
variableDeclaration();
setState(79);
match(Semi);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class FunctionParametersContext extends ParserRuleContext {
public List<VariableDeclarationContext> variableDeclaration() {
return getRuleContexts(VariableDeclarationContext.class);
}
public VariableDeclarationContext variableDeclaration(int i) {
return getRuleContext(VariableDeclarationContext.class, i);
}
public FunctionParametersContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_functionParameters;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterFunctionParameters(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitFunctionParameters(this);
}
}
public final FunctionParametersContext functionParameters() throws RecognitionException {
FunctionParametersContext _localctx = new FunctionParametersContext(_ctx, getState());
enterRule(_localctx, 12, RULE_functionParameters);
try {
int _alt;
enterOuterAlt(_localctx, 1);
{
setState(86);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 4, _ctx);
while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER) {
if (_alt == 1) {
{
{
setState(81);
variableDeclaration();
setState(82);
match(Comma);
}
}
}
setState(88);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 4, _ctx);
}
setState(89);
variableDeclaration();
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ClassBlockContext extends ParserRuleContext {
public List<ClassBlockItemContext> classBlockItem() {
return getRuleContexts(ClassBlockItemContext.class);
}
public ClassBlockItemContext classBlockItem(int i) {
return getRuleContext(ClassBlockItemContext.class, i);
}
public ClassBlockContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_classBlock;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterClassBlock(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitClassBlock(this);
}
}
public final ClassBlockContext classBlock() throws RecognitionException {
ClassBlockContext _localctx = new ClassBlockContext(_ctx, getState());
enterRule(_localctx, 14, RULE_classBlock);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(91);
match(LBrace);
setState(95);
_errHandler.sync(this);
_la = _input.LA(1);
while ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << Bool)
| (1L << Int)
| (1L << String)
| (1L << Void)
| (1L << Identifier)))
!= 0)) {
{
{
setState(92);
classBlockItem();
}
}
setState(97);
_errHandler.sync(this);
_la = _input.LA(1);
}
setState(98);
match(RBrace);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ClassBlockItemContext extends ParserRuleContext {
public ClassBlockItemContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_classBlockItem;
}
public ClassBlockItemContext() {
}
public void copyFrom(ClassBlockItemContext ctx) {
super.copyFrom(ctx);
}
}
public static class ClassCstrDeclContext extends ClassBlockItemContext {
public ConstructorDeclarationContext constructorDeclaration() {
return getRuleContext(ConstructorDeclarationContext.class, 0);
}
public ClassCstrDeclContext(ClassBlockItemContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterClassCstrDecl(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitClassCstrDecl(this);
}
}
public static class ClassFuncDeclContext extends ClassBlockItemContext {
public FunctionDeclarationContext functionDeclaration() {
return getRuleContext(FunctionDeclarationContext.class, 0);
}
public ClassFuncDeclContext(ClassBlockItemContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterClassFuncDecl(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitClassFuncDecl(this);
}
}
public static class ClassVarDeclContext extends ClassBlockItemContext {
public VariableDeclarationStatementContext variableDeclarationStatement() {
return getRuleContext(VariableDeclarationStatementContext.class, 0);
}
public ClassVarDeclContext(ClassBlockItemContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterClassVarDecl(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitClassVarDecl(this);
}
}
public final ClassBlockItemContext classBlockItem() throws RecognitionException {
ClassBlockItemContext _localctx = new ClassBlockItemContext(_ctx, getState());
enterRule(_localctx, 16, RULE_classBlockItem);
try {
setState(103);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 6, _ctx)) {
case 1:
_localctx = new ClassVarDeclContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(100);
variableDeclarationStatement();
}
break;
case 2:
_localctx = new ClassCstrDeclContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(101);
constructorDeclaration();
}
break;
case 3:
_localctx = new ClassFuncDeclContext(_localctx);
enterOuterAlt(_localctx, 3);
{
setState(102);
functionDeclaration();
}
break;
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ConstructorDeclarationContext extends ParserRuleContext {
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public BlockStatementContext blockStatement() {
return getRuleContext(BlockStatementContext.class, 0);
}
public FunctionParametersContext functionParameters() {
return getRuleContext(FunctionParametersContext.class, 0);
}
public ConstructorDeclarationContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_constructorDeclaration;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterConstructorDeclaration(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitConstructorDeclaration(this);
}
}
public final ConstructorDeclarationContext constructorDeclaration() throws RecognitionException {
ConstructorDeclarationContext _localctx = new ConstructorDeclarationContext(_ctx, getState());
enterRule(_localctx, 18, RULE_constructorDeclaration);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(105);
match(Identifier);
setState(106);
match(LParen);
setState(108);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << Bool)
| (1L << Int)
| (1L << String)
| (1L << Void)
| (1L << Identifier)))
!= 0)) {
{
setState(107);
functionParameters();
}
}
setState(110);
match(RParen);
setState(111);
blockStatement();
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class StatementContext extends ParserRuleContext {
public StatementContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_statement;
}
public StatementContext() {
}
public void copyFrom(StatementContext ctx) {
super.copyFrom(ctx);
}
}
public static class BranchStmtContext extends StatementContext {
public BranchStatementContext branchStatement() {
return getRuleContext(BranchStatementContext.class, 0);
}
public BranchStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBranchStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBranchStmt(this);
}
}
public static class LoopStmtContext extends StatementContext {
public LoopStatementContext loopStatement() {
return getRuleContext(LoopStatementContext.class, 0);
}
public LoopStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterLoopStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitLoopStmt(this);
}
}
public static class ExprStmtContext extends StatementContext {
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public ExprStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterExprStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitExprStmt(this);
}
}
public static class JumpStmtContext extends StatementContext {
public JumpStatementContext jumpStatement() {
return getRuleContext(JumpStatementContext.class, 0);
}
public JumpStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterJumpStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitJumpStmt(this);
}
}
public static class VarDeclStmtContext extends StatementContext {
public VariableDeclarationStatementContext variableDeclarationStatement() {
return getRuleContext(VariableDeclarationStatementContext.class, 0);
}
public VarDeclStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterVarDeclStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitVarDeclStmt(this);
}
}
public static class BlockStmtContext extends StatementContext {
public BlockStatementContext blockStatement() {
return getRuleContext(BlockStatementContext.class, 0);
}
public BlockStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBlockStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBlockStmt(this);
}
}
public static class EmptyStmtContext extends StatementContext {
public EmptyStmtContext(StatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterEmptyStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitEmptyStmt(this);
}
}
public final StatementContext statement() throws RecognitionException {
StatementContext _localctx = new StatementContext(_ctx, getState());
enterRule(_localctx, 20, RULE_statement);
try {
setState(122);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 8, _ctx)) {
case 1:
_localctx = new BlockStmtContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(113);
blockStatement();
}
break;
case 2:
_localctx = new VarDeclStmtContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(114);
variableDeclarationStatement();
}
break;
case 3:
_localctx = new BranchStmtContext(_localctx);
enterOuterAlt(_localctx, 3);
{
setState(115);
branchStatement();
}
break;
case 4:
_localctx = new LoopStmtContext(_localctx);
enterOuterAlt(_localctx, 4);
{
setState(116);
loopStatement();
}
break;
case 5:
_localctx = new ExprStmtContext(_localctx);
enterOuterAlt(_localctx, 5);
{
setState(117);
expression(0);
setState(118);
match(Semi);
}
break;
case 6:
_localctx = new JumpStmtContext(_localctx);
enterOuterAlt(_localctx, 6);
{
setState(120);
jumpStatement();
}
break;
case 7:
_localctx = new EmptyStmtContext(_localctx);
enterOuterAlt(_localctx, 7);
{
setState(121);
match(Semi);
}
break;
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class BlockStatementContext extends ParserRuleContext {
public List<StatementContext> statement() {
return getRuleContexts(StatementContext.class);
}
public StatementContext statement(int i) {
return getRuleContext(StatementContext.class, i);
}
public BlockStatementContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_blockStatement;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBlockStatement(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBlockStatement(this);
}
}
public final BlockStatementContext blockStatement() throws RecognitionException {
BlockStatementContext _localctx = new BlockStatementContext(_ctx, getState());
enterRule(_localctx, 22, RULE_blockStatement);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(124);
match(LBrace);
setState(128);
_errHandler.sync(this);
_la = _input.LA(1);
while ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << Bool)
| (1L << Int)
| (1L << String)
| (1L << Void)
| (1L << If)
| (1L << For)
| (1L << While)
| (1L << Break)
| (1L << Continue)
| (1L << Return)
| (1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << Semi)
| (1L << LParen)
| (1L << LBrace)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
{
setState(125);
statement();
}
}
setState(130);
_errHandler.sync(this);
_la = _input.LA(1);
}
setState(131);
match(RBrace);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class BranchStatementContext extends ParserRuleContext {
public TerminalNode If() {
return getToken(MParser.If, 0);
}
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public List<StatementContext> statement() {
return getRuleContexts(StatementContext.class);
}
public StatementContext statement(int i) {
return getRuleContext(StatementContext.class, i);
}
public TerminalNode Else() {
return getToken(MParser.Else, 0);
}
public BranchStatementContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_branchStatement;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBranchStatement(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBranchStatement(this);
}
}
public final BranchStatementContext branchStatement() throws RecognitionException {
BranchStatementContext _localctx = new BranchStatementContext(_ctx, getState());
enterRule(_localctx, 24, RULE_branchStatement);
try {
enterOuterAlt(_localctx, 1);
{
setState(133);
match(If);
setState(134);
match(LParen);
setState(135);
expression(0);
setState(136);
match(RParen);
setState(137);
statement();
setState(140);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 10, _ctx)) {
case 1: {
setState(138);
match(Else);
setState(139);
statement();
}
break;
}
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class LoopStatementContext extends ParserRuleContext {
public LoopStatementContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_loopStatement;
}
public LoopStatementContext() {
}
public void copyFrom(LoopStatementContext ctx) {
super.copyFrom(ctx);
}
}
public static class WhileStmtContext extends LoopStatementContext {
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public StatementContext statement() {
return getRuleContext(StatementContext.class, 0);
}
public WhileStmtContext(LoopStatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterWhileStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitWhileStmt(this);
}
}
public static class ForStmtContext extends LoopStatementContext {
public ExpressionContext init;
public ExpressionContext cond;
public ExpressionContext step;
public StatementContext statement() {
return getRuleContext(StatementContext.class, 0);
}
public List<ExpressionContext> expression() {
return getRuleContexts(ExpressionContext.class);
}
public ExpressionContext expression(int i) {
return getRuleContext(ExpressionContext.class, i);
}
public ForStmtContext(LoopStatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterForStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitForStmt(this);
}
}
public final LoopStatementContext loopStatement() throws RecognitionException {
LoopStatementContext _localctx = new LoopStatementContext(_ctx, getState());
enterRule(_localctx, 26, RULE_loopStatement);
int _la;
try {
setState(163);
_errHandler.sync(this);
switch (_input.LA(1)) {
case For:
_localctx = new ForStmtContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(142);
match(For);
setState(143);
match(LParen);
setState(145);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << LParen)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
setState(144);
((ForStmtContext) _localctx).init = expression(0);
}
}
setState(147);
match(Semi);
setState(149);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << LParen)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
setState(148);
((ForStmtContext) _localctx).cond = expression(0);
}
}
setState(151);
match(Semi);
setState(153);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << LParen)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
setState(152);
((ForStmtContext) _localctx).step = expression(0);
}
}
setState(155);
match(RParen);
setState(156);
statement();
}
break;
case While:
_localctx = new WhileStmtContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(157);
match(While);
setState(158);
match(LParen);
setState(159);
expression(0);
setState(160);
match(RParen);
setState(161);
statement();
}
break;
default:
throw new NoViableAltException(this);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class JumpStatementContext extends ParserRuleContext {
public JumpStatementContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_jumpStatement;
}
public JumpStatementContext() {
}
public void copyFrom(JumpStatementContext ctx) {
super.copyFrom(ctx);
}
}
public static class ContinueStmtContext extends JumpStatementContext {
public ContinueStmtContext(JumpStatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterContinueStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitContinueStmt(this);
}
}
public static class BreakStmtContext extends JumpStatementContext {
public BreakStmtContext(JumpStatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBreakStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBreakStmt(this);
}
}
public static class ReturnStmtContext extends JumpStatementContext {
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public ReturnStmtContext(JumpStatementContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterReturnStmt(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitReturnStmt(this);
}
}
public final JumpStatementContext jumpStatement() throws RecognitionException {
JumpStatementContext _localctx = new JumpStatementContext(_ctx, getState());
enterRule(_localctx, 28, RULE_jumpStatement);
int _la;
try {
setState(174);
_errHandler.sync(this);
switch (_input.LA(1)) {
case Return:
_localctx = new ReturnStmtContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(165);
match(Return);
setState(167);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << LParen)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
setState(166);
expression(0);
}
}
setState(169);
match(Semi);
}
break;
case Break:
_localctx = new BreakStmtContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(170);
match(Break);
setState(171);
match(Semi);
}
break;
case Continue:
_localctx = new ContinueStmtContext(_localctx);
enterOuterAlt(_localctx, 3);
{
setState(172);
match(Continue);
setState(173);
match(Semi);
}
break;
default:
throw new NoViableAltException(this);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ClassTypeContext extends ParserRuleContext {
public ClassTypeContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_classType;
}
public ClassTypeContext() {
}
public void copyFrom(ClassTypeContext ctx) {
super.copyFrom(ctx);
}
}
public static class ArrayTypeContext extends ClassTypeContext {
public ArrayClassContext arrayClass() {
return getRuleContext(ArrayClassContext.class, 0);
}
public ArrayTypeContext(ClassTypeContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterArrayType(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitArrayType(this);
}
}
public static class NonArrayTypeContext extends ClassTypeContext {
public NonArrayClassContext nonArrayClass() {
return getRuleContext(NonArrayClassContext.class, 0);
}
public NonArrayTypeContext(ClassTypeContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterNonArrayType(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitNonArrayType(this);
}
}
public final ClassTypeContext classType() throws RecognitionException {
ClassTypeContext _localctx = new ClassTypeContext(_ctx, getState());
enterRule(_localctx, 30, RULE_classType);
try {
setState(178);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 17, _ctx)) {
case 1:
_localctx = new ArrayTypeContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(176);
arrayClass();
}
break;
case 2:
_localctx = new NonArrayTypeContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(177);
nonArrayClass();
}
break;
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ArrayClassContext extends ParserRuleContext {
public NonArrayClassContext nonArrayClass() {
return getRuleContext(NonArrayClassContext.class, 0);
}
public List<BracketsContext> brackets() {
return getRuleContexts(BracketsContext.class);
}
public BracketsContext brackets(int i) {
return getRuleContext(BracketsContext.class, i);
}
public ArrayClassContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_arrayClass;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterArrayClass(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitArrayClass(this);
}
}
public final ArrayClassContext arrayClass() throws RecognitionException {
ArrayClassContext _localctx = new ArrayClassContext(_ctx, getState());
enterRule(_localctx, 32, RULE_arrayClass);
int _la;
try {
enterOuterAlt(_localctx, 1);
{
setState(180);
nonArrayClass();
setState(182);
_errHandler.sync(this);
_la = _input.LA(1);
do {
{
{
setState(181);
brackets();
}
}
setState(184);
_errHandler.sync(this);
_la = _input.LA(1);
} while (_la == LBracket);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class NonArrayClassContext extends ParserRuleContext {
public Token type;
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public NonArrayClassContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_nonArrayClass;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterNonArrayClass(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitNonArrayClass(this);
}
}
public final NonArrayClassContext nonArrayClass() throws RecognitionException {
NonArrayClassContext _localctx = new NonArrayClassContext(_ctx, getState());
enterRule(_localctx, 34, RULE_nonArrayClass);
try {
setState(191);
_errHandler.sync(this);
switch (_input.LA(1)) {
case Bool:
enterOuterAlt(_localctx, 1);
{
setState(186);
((NonArrayClassContext) _localctx).type = match(Bool);
}
break;
case Int:
enterOuterAlt(_localctx, 2);
{
setState(187);
((NonArrayClassContext) _localctx).type = match(Int);
}
break;
case Void:
enterOuterAlt(_localctx, 3);
{
setState(188);
((NonArrayClassContext) _localctx).type = match(Void);
}
break;
case String:
enterOuterAlt(_localctx, 4);
{
setState(189);
((NonArrayClassContext) _localctx).type = match(String);
}
break;
case Identifier:
enterOuterAlt(_localctx, 5);
{
setState(190);
((NonArrayClassContext) _localctx).type = match(Identifier);
}
break;
default:
throw new NoViableAltException(this);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ExpressionContext extends ParserRuleContext {
public ExpressionContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_expression;
}
public ExpressionContext() {
}
public void copyFrom(ExpressionContext ctx) {
super.copyFrom(ctx);
}
}
public static class IdentifierContext extends ExpressionContext {
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public IdentifierContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterIdentifier(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitIdentifier(this);
}
}
public static class MemberAcessContext extends ExpressionContext {
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public TerminalNode Identifier() {
return getToken(MParser.Identifier, 0);
}
public MemberAcessContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterMemberAcess(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitMemberAcess(this);
}
}
public static class ArrayAcessContext extends ExpressionContext {
public List<ExpressionContext> expression() {
return getRuleContexts(ExpressionContext.class);
}
public ExpressionContext expression(int i) {
return getRuleContext(ExpressionContext.class, i);
}
public ArrayAcessContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterArrayAcess(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitArrayAcess(this);
}
}
public static class ConstContext extends ExpressionContext {
public ConstantContext constant() {
return getRuleContext(ConstantContext.class, 0);
}
public ConstContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterConst(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitConst(this);
}
}
public static class SubExprContext extends ExpressionContext {
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public SubExprContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterSubExpr(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitSubExpr(this);
}
}
public static class BinaryExprContext extends ExpressionContext {
public Token op;
public List<ExpressionContext> expression() {
return getRuleContexts(ExpressionContext.class);
}
public ExpressionContext expression(int i) {
return getRuleContext(ExpressionContext.class, i);
}
public BinaryExprContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBinaryExpr(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBinaryExpr(this);
}
}
public static class NewExprContext extends ExpressionContext {
public NewObjectContext newObject() {
return getRuleContext(NewObjectContext.class, 0);
}
public NewExprContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterNewExpr(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitNewExpr(this);
}
}
public static class FunctionCallContext extends ExpressionContext {
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public CallParameterContext callParameter() {
return getRuleContext(CallParameterContext.class, 0);
}
public FunctionCallContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterFunctionCall(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitFunctionCall(this);
}
}
public static class PostfixIncDecContext extends ExpressionContext {
public Token op;
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public PostfixIncDecContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterPostfixIncDec(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitPostfixIncDec(this);
}
}
public static class UnaryExprContext extends ExpressionContext {
public Token op;
public ExpressionContext expression() {
return getRuleContext(ExpressionContext.class, 0);
}
public UnaryExprContext(ExpressionContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterUnaryExpr(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitUnaryExpr(this);
}
}
public final ExpressionContext expression() throws RecognitionException {
return expression(0);
}
private ExpressionContext expression(int _p) throws RecognitionException {
ParserRuleContext _parentctx = _ctx;
int _parentState = getState();
ExpressionContext _localctx = new ExpressionContext(_ctx, _parentState);
ExpressionContext _prevctx = _localctx;
int _startState = 36;
enterRecursionRule(_localctx, 36, RULE_expression, _p);
int _la;
try {
int _alt;
enterOuterAlt(_localctx, 1);
{
setState(208);
_errHandler.sync(this);
switch (_input.LA(1)) {
case AddAdd:
case SubSub: {
_localctx = new UnaryExprContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(194);
((UnaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == AddAdd || _la == SubSub)) {
((UnaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(195);
expression(18);
}
break;
case Add:
case Sub: {
_localctx = new UnaryExprContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(196);
((UnaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == Add || _la == Sub)) {
((UnaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(197);
expression(17);
}
break;
case Not:
case BNot: {
_localctx = new UnaryExprContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(198);
((UnaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == Not || _la == BNot)) {
((UnaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(199);
expression(16);
}
break;
case New: {
_localctx = new NewExprContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(200);
match(New);
setState(201);
newObject();
}
break;
case Identifier: {
_localctx = new IdentifierContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(202);
match(Identifier);
}
break;
case BoolConst:
case NumConst:
case StrConst:
case NullConst: {
_localctx = new ConstContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(203);
constant();
}
break;
case LParen: {
_localctx = new SubExprContext(_localctx);
_ctx = _localctx;
_prevctx = _localctx;
setState(204);
match(LParen);
setState(205);
expression(0);
setState(206);
match(RParen);
}
break;
default:
throw new NoViableAltException(this);
}
_ctx.stop = _input.LT(-1);
setState(261);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 23, _ctx);
while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER) {
if (_alt == 1) {
if (_parseListeners != null) triggerExitRuleEvent();
_prevctx = _localctx;
{
setState(259);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 22, _ctx)) {
case 1: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(210);
if (!(precpred(_ctx, 14)))
throw new FailedPredicateException(this, "precpred(_ctx, 14)");
setState(211);
((BinaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!((((_la) & ~0x3f) == 0
&& ((1L << _la) & ((1L << Mul) | (1L << Div) | (1L << Mod))) != 0))) {
((BinaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(212);
expression(15);
}
break;
case 2: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(213);
if (!(precpred(_ctx, 13)))
throw new FailedPredicateException(this, "precpred(_ctx, 13)");
setState(214);
((BinaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == Add || _la == Sub)) {
((BinaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(215);
expression(14);
}
break;
case 3: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(216);
if (!(precpred(_ctx, 12)))
throw new FailedPredicateException(this, "precpred(_ctx, 12)");
setState(217);
((BinaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == LShift || _la == RShift)) {
((BinaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(218);
expression(13);
}
break;
case 4: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(219);
if (!(precpred(_ctx, 11)))
throw new FailedPredicateException(this, "precpred(_ctx, 11)");
setState(220);
((BinaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!((((_la) & ~0x3f) == 0
&& ((1L << _la) & ((1L << LT) | (1L << GT) | (1L << LE) | (1L << GE)))
!= 0))) {
((BinaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(221);
expression(12);
}
break;
case 5: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(222);
if (!(precpred(_ctx, 10)))
throw new FailedPredicateException(this, "precpred(_ctx, 10)");
setState(223);
((BinaryExprContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == EQ || _la == NE)) {
((BinaryExprContext) _localctx).op = (Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
setState(224);
expression(11);
}
break;
case 6: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(225);
if (!(precpred(_ctx, 9)))
throw new FailedPredicateException(this, "precpred(_ctx, 9)");
setState(226);
((BinaryExprContext) _localctx).op = match(BAnd);
setState(227);
expression(10);
}
break;
case 7: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(228);
if (!(precpred(_ctx, 8)))
throw new FailedPredicateException(this, "precpred(_ctx, 8)");
setState(229);
((BinaryExprContext) _localctx).op = match(BXor);
setState(230);
expression(9);
}
break;
case 8: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(231);
if (!(precpred(_ctx, 7)))
throw new FailedPredicateException(this, "precpred(_ctx, 7)");
setState(232);
((BinaryExprContext) _localctx).op = match(BOr);
setState(233);
expression(8);
}
break;
case 9: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(234);
if (!(precpred(_ctx, 6)))
throw new FailedPredicateException(this, "precpred(_ctx, 6)");
setState(235);
((BinaryExprContext) _localctx).op = match(And);
setState(236);
expression(7);
}
break;
case 10: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(237);
if (!(precpred(_ctx, 5)))
throw new FailedPredicateException(this, "precpred(_ctx, 5)");
setState(238);
((BinaryExprContext) _localctx).op = match(Or);
setState(239);
expression(6);
}
break;
case 11: {
_localctx =
new BinaryExprContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(240);
if (!(precpred(_ctx, 4)))
throw new FailedPredicateException(this, "precpred(_ctx, 4)");
setState(241);
((BinaryExprContext) _localctx).op = match(Assign);
setState(242);
expression(4);
}
break;
case 12: {
_localctx =
new PostfixIncDecContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(243);
if (!(precpred(_ctx, 22)))
throw new FailedPredicateException(this, "precpred(_ctx, 22)");
setState(244);
((PostfixIncDecContext) _localctx).op = _input.LT(1);
_la = _input.LA(1);
if (!(_la == AddAdd || _la == SubSub)) {
((PostfixIncDecContext) _localctx).op =
(Token) _errHandler.recoverInline(this);
} else {
if (_input.LA(1) == Token.EOF) matchedEOF = true;
_errHandler.reportMatch(this);
consume();
}
}
break;
case 13: {
_localctx =
new FunctionCallContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(245);
if (!(precpred(_ctx, 21)))
throw new FailedPredicateException(this, "precpred(_ctx, 21)");
setState(246);
match(LParen);
setState(248);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << LParen)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
setState(247);
callParameter();
}
}
setState(250);
match(RParen);
}
break;
case 14: {
_localctx =
new ArrayAcessContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(251);
if (!(precpred(_ctx, 20)))
throw new FailedPredicateException(this, "precpred(_ctx, 20)");
setState(252);
match(LBracket);
setState(253);
expression(0);
setState(254);
match(RBracket);
}
break;
case 15: {
_localctx =
new MemberAcessContext(new ExpressionContext(_parentctx, _parentState));
pushNewRecursionContext(_localctx, _startState, RULE_expression);
setState(256);
if (!(precpred(_ctx, 19)))
throw new FailedPredicateException(this, "precpred(_ctx, 19)");
setState(257);
match(Dot);
setState(258);
match(Identifier);
}
break;
}
}
}
setState(263);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 23, _ctx);
}
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
unrollRecursionContexts(_parentctx);
}
return _localctx;
}
public static class CallParameterContext extends ParserRuleContext {
public List<ExpressionContext> expression() {
return getRuleContexts(ExpressionContext.class);
}
public ExpressionContext expression(int i) {
return getRuleContext(ExpressionContext.class, i);
}
public CallParameterContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_callParameter;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterCallParameter(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitCallParameter(this);
}
}
public final CallParameterContext callParameter() throws RecognitionException {
CallParameterContext _localctx = new CallParameterContext(_ctx, getState());
enterRule(_localctx, 38, RULE_callParameter);
try {
int _alt;
enterOuterAlt(_localctx, 1);
{
setState(269);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 24, _ctx);
while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER) {
if (_alt == 1) {
{
{
setState(264);
expression(0);
setState(265);
match(Comma);
}
}
}
setState(271);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 24, _ctx);
}
setState(272);
expression(0);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class NewObjectContext extends ParserRuleContext {
public NewObjectContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_newObject;
}
public NewObjectContext() {
}
public void copyFrom(NewObjectContext ctx) {
super.copyFrom(ctx);
}
}
public static class NewArrayContext extends NewObjectContext {
public NonArrayClassContext nonArrayClass() {
return getRuleContext(NonArrayClassContext.class, 0);
}
public List<ExpressionContext> expression() {
return getRuleContexts(ExpressionContext.class);
}
public ExpressionContext expression(int i) {
return getRuleContext(ExpressionContext.class, i);
}
public List<BracketsContext> brackets() {
return getRuleContexts(BracketsContext.class);
}
public BracketsContext brackets(int i) {
return getRuleContext(BracketsContext.class, i);
}
public NewArrayContext(NewObjectContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterNewArray(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitNewArray(this);
}
}
public static class NewNonArrayContext extends NewObjectContext {
public NonArrayClassContext nonArrayClass() {
return getRuleContext(NonArrayClassContext.class, 0);
}
public CallParameterContext callParameter() {
return getRuleContext(CallParameterContext.class, 0);
}
public NewNonArrayContext(NewObjectContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterNewNonArray(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitNewNonArray(this);
}
}
public static class NewErrorContext extends NewObjectContext {
public NonArrayClassContext nonArrayClass() {
return getRuleContext(NonArrayClassContext.class, 0);
}
public List<ExpressionContext> expression() {
return getRuleContexts(ExpressionContext.class);
}
public ExpressionContext expression(int i) {
return getRuleContext(ExpressionContext.class, i);
}
public List<BracketsContext> brackets() {
return getRuleContexts(BracketsContext.class);
}
public BracketsContext brackets(int i) {
return getRuleContext(BracketsContext.class, i);
}
public NewErrorContext(NewObjectContext ctx) {
copyFrom(ctx);
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterNewError(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitNewError(this);
}
}
public final NewObjectContext newObject() throws RecognitionException {
NewObjectContext _localctx = new NewObjectContext(_ctx, getState());
enterRule(_localctx, 40, RULE_newObject);
int _la;
try {
int _alt;
setState(319);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 32, _ctx)) {
case 1:
_localctx = new NewErrorContext(_localctx);
enterOuterAlt(_localctx, 1);
{
setState(274);
nonArrayClass();
setState(279);
_errHandler.sync(this);
_alt = 1;
do {
switch (_alt) {
case 1: {
{
setState(275);
match(LBracket);
setState(276);
expression(0);
setState(277);
match(RBracket);
}
}
break;
default:
throw new NoViableAltException(this);
}
setState(281);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 25, _ctx);
} while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER);
setState(284);
_errHandler.sync(this);
_alt = 1;
do {
switch (_alt) {
case 1: {
{
setState(283);
brackets();
}
}
break;
default:
throw new NoViableAltException(this);
}
setState(286);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 26, _ctx);
} while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER);
setState(292);
_errHandler.sync(this);
_alt = 1;
do {
switch (_alt) {
case 1: {
{
setState(288);
match(LBracket);
setState(289);
expression(0);
setState(290);
match(RBracket);
}
}
break;
default:
throw new NoViableAltException(this);
}
setState(294);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 27, _ctx);
} while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER);
}
break;
case 2:
_localctx = new NewArrayContext(_localctx);
enterOuterAlt(_localctx, 2);
{
setState(296);
nonArrayClass();
setState(301);
_errHandler.sync(this);
_alt = 1;
do {
switch (_alt) {
case 1: {
{
setState(297);
match(LBracket);
setState(298);
expression(0);
setState(299);
match(RBracket);
}
}
break;
default:
throw new NoViableAltException(this);
}
setState(303);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 28, _ctx);
} while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER);
setState(308);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 29, _ctx);
while (_alt != 2 && _alt != org.antlr.v4.runtime.atn.ATN.INVALID_ALT_NUMBER) {
if (_alt == 1) {
{
{
setState(305);
brackets();
}
}
}
setState(310);
_errHandler.sync(this);
_alt = getInterpreter().adaptivePredict(_input, 29, _ctx);
}
}
break;
case 3:
_localctx = new NewNonArrayContext(_localctx);
enterOuterAlt(_localctx, 3);
{
setState(311);
nonArrayClass();
setState(317);
_errHandler.sync(this);
switch (getInterpreter().adaptivePredict(_input, 31, _ctx)) {
case 1: {
setState(312);
match(LParen);
setState(314);
_errHandler.sync(this);
_la = _input.LA(1);
if ((((_la) & ~0x3f) == 0
&& ((1L << _la)
& ((1L << New)
| (1L << Add)
| (1L << Sub)
| (1L << Not)
| (1L << BNot)
| (1L << AddAdd)
| (1L << SubSub)
| (1L << LParen)
| (1L << BoolConst)
| (1L << NumConst)
| (1L << StrConst)
| (1L << NullConst)
| (1L << Identifier)))
!= 0)) {
{
setState(313);
callParameter();
}
}
setState(316);
match(RParen);
}
break;
}
}
break;
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class BracketsContext extends ParserRuleContext {
public BracketsContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_brackets;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterBrackets(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitBrackets(this);
}
}
public final BracketsContext brackets() throws RecognitionException {
BracketsContext _localctx = new BracketsContext(_ctx, getState());
enterRule(_localctx, 42, RULE_brackets);
try {
enterOuterAlt(_localctx, 1);
{
setState(321);
match(LBracket);
setState(322);
match(RBracket);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public static class ConstantContext extends ParserRuleContext {
public Token type;
public TerminalNode BoolConst() {
return getToken(MParser.BoolConst, 0);
}
public TerminalNode NumConst() {
return getToken(MParser.NumConst, 0);
}
public TerminalNode StrConst() {
return getToken(MParser.StrConst, 0);
}
public TerminalNode NullConst() {
return getToken(MParser.NullConst, 0);
}
public ConstantContext(ParserRuleContext parent, int invokingState) {
super(parent, invokingState);
}
@Override
public int getRuleIndex() {
return RULE_constant;
}
@Override
public void enterRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).enterConstant(this);
}
@Override
public void exitRule(ParseTreeListener listener) {
if (listener instanceof MListener) ((MListener) listener).exitConstant(this);
}
}
public final ConstantContext constant() throws RecognitionException {
ConstantContext _localctx = new ConstantContext(_ctx, getState());
enterRule(_localctx, 44, RULE_constant);
try {
setState(328);
_errHandler.sync(this);
switch (_input.LA(1)) {
case BoolConst:
enterOuterAlt(_localctx, 1);
{
setState(324);
((ConstantContext) _localctx).type = match(BoolConst);
}
break;
case NumConst:
enterOuterAlt(_localctx, 2);
{
setState(325);
((ConstantContext) _localctx).type = match(NumConst);
}
break;
case StrConst:
enterOuterAlt(_localctx, 3);
{
setState(326);
((ConstantContext) _localctx).type = match(StrConst);
}
break;
case NullConst:
enterOuterAlt(_localctx, 4);
{
setState(327);
((ConstantContext) _localctx).type = match(NullConst);
}
break;
default:
throw new NoViableAltException(this);
}
} catch (RecognitionException re) {
_localctx.exception = re;
_errHandler.reportError(this, re);
_errHandler.recover(this, re);
} finally {
exitRule();
}
return _localctx;
}
public boolean sempred(RuleContext _localctx, int ruleIndex, int predIndex) {
switch (ruleIndex) {
case 18:
return expression_sempred((ExpressionContext) _localctx, predIndex);
}
return true;
}
private boolean expression_sempred(ExpressionContext _localctx, int predIndex) {
switch (predIndex) {
case 0:
return precpred(_ctx, 14);
case 1:
return precpred(_ctx, 13);
case 2:
return precpred(_ctx, 12);
case 3:
return precpred(_ctx, 11);
case 4:
return precpred(_ctx, 10);
case 5:
return precpred(_ctx, 9);
case 6:
return precpred(_ctx, 8);
case 7:
return precpred(_ctx, 7);
case 8:
return precpred(_ctx, 6);
case 9:
return precpred(_ctx, 5);
case 10:
return precpred(_ctx, 4);
case 11:
return precpred(_ctx, 22);
case 12:
return precpred(_ctx, 21);
case 13:
return precpred(_ctx, 20);
case 14:
return precpred(_ctx, 19);
}
return true;
}
public static final String _serializedATN =
"\3\u608b\ua72a\u8133\ub9ed\u417c\u3be7\u7786\u5964\3\67\u014d\4\2\t\2"
+ "\4\3\t\3\4\4\t\4\4\5\t\5\4\6\t\6\4\7\t\7\4\b\t\b\4\t\t\t\4\n\t\n\4\13"
+ "\t\13\4\f\t\f\4\r\t\r\4\16\t\16\4\17\t\17\4\20\t\20\4\21\t\21\4\22\t\22"
+ "\4\23\t\23\4\24\t\24\4\25\t\25\4\26\t\26\4\27\t\27\4\30\t\30\3\2\7\2\62"
+ "\n\2\f\2\16\2\65\13\2\3\2\3\2\3\3\3\3\3\3\5\3<\n\3\3\4\3\4\3\4\3\4\3\5"
+ "\3\5\3\5\3\5\5\5F\n\5\3\5\3\5\3\5\3\6\3\6\3\6\3\6\5\6O\n\6\3\7\3\7\3\7"
+ "\3\b\3\b\3\b\7\bW\n\b\f\b\16\bZ\13\b\3\b\3\b\3\t\3\t\7\t`\n\t\f\t\16\t"
+ "c\13\t\3\t\3\t\3\n\3\n\3\n\5\nj\n\n\3\13\3\13\3\13\5\13o\n\13\3\13\3\13"
+ "\3\13\3\f\3\f\3\f\3\f\3\f\3\f\3\f\3\f\3\f\5\f}\n\f\3\r\3\r\7\r\u0081\n"
+ "\r\f\r\16\r\u0084\13\r\3\r\3\r\3\16\3\16\3\16\3\16\3\16\3\16\3\16\5\16"
+ "\u008f\n\16\3\17\3\17\3\17\5\17\u0094\n\17\3\17\3\17\5\17\u0098\n\17\3"
+ "\17\3\17\5\17\u009c\n\17\3\17\3\17\3\17\3\17\3\17\3\17\3\17\3\17\5\17"
+ "\u00a6\n\17\3\20\3\20\5\20\u00aa\n\20\3\20\3\20\3\20\3\20\3\20\5\20\u00b1"
+ "\n\20\3\21\3\21\5\21\u00b5\n\21\3\22\3\22\6\22\u00b9\n\22\r\22\16\22\u00ba"
+ "\3\23\3\23\3\23\3\23\3\23\5\23\u00c2\n\23\3\24\3\24\3\24\3\24\3\24\3\24"
+ "\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\5\24\u00d3\n\24\3\24\3\24"
+ "\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24"
+ "\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24"
+ "\3\24\3\24\3\24\3\24\3\24\3\24\3\24\3\24\5\24\u00fb\n\24\3\24\3\24\3\24"
+ "\3\24\3\24\3\24\3\24\3\24\3\24\7\24\u0106\n\24\f\24\16\24\u0109\13\24"
+ "\3\25\3\25\3\25\7\25\u010e\n\25\f\25\16\25\u0111\13\25\3\25\3\25\3\26"
+ "\3\26\3\26\3\26\3\26\6\26\u011a\n\26\r\26\16\26\u011b\3\26\6\26\u011f"
+ "\n\26\r\26\16\26\u0120\3\26\3\26\3\26\3\26\6\26\u0127\n\26\r\26\16\26"
+ "\u0128\3\26\3\26\3\26\3\26\3\26\6\26\u0130\n\26\r\26\16\26\u0131\3\26"
+ "\7\26\u0135\n\26\f\26\16\26\u0138\13\26\3\26\3\26\3\26\5\26\u013d\n\26"
+ "\3\26\5\26\u0140\n\26\5\26\u0142\n\26\3\27\3\27\3\27\3\30\3\30\3\30\3"
+ "\30\5\30\u014b\n\30\3\30\2\3&\31\2\4\6\b\n\f\16\20\22\24\26\30\32\34\36"
+ " \"$&(*,.\2\t\3\2%&\3\2\20\21\4\2\35\35 \3\2\22\24\3\2\36\37\3\2\25\30"
+ "\3\2\31\32\2\u0177\2\63\3\2\2\2\4;\3\2\2\2\6=\3\2\2\2\bA\3\2\2\2\nJ\3"
+ "\2\2\2\fP\3\2\2\2\16X\3\2\2\2\20]\3\2\2\2\22i\3\2\2\2\24k\3\2\2\2\26|"
+ "\3\2\2\2\30~\3\2\2\2\32\u0087\3\2\2\2\34\u00a5\3\2\2\2\36\u00b0\3\2\2"
+ "\2 \u00b4\3\2\2\2\"\u00b6\3\2\2\2$\u00c1\3\2\2\2&\u00d2\3\2\2\2(\u010f"
+ "\3\2\2\2*\u0141\3\2\2\2,\u0143\3\2\2\2.\u014a\3\2\2\2\60\62\5\4\3\2\61"
+ "\60\3\2\2\2\62\65\3\2\2\2\63\61\3\2\2\2\63\64\3\2\2\2\64\66\3\2\2\2\65"
+ "\63\3\2\2\2\66\67\7\2\2\3\67\3\3\2\2\28<\5\6\4\29<\5\b\5\2:<\5\f\7\2;"
+ "8\3\2\2\2;9\3\2\2\2;:\3\2\2\2<\5\3\2\2\2=>\7\17\2\2>?\7\64\2\2?@\5\20"
+ "\t\2@\7\3\2\2\2AB\5 \21\2BC\7\64\2\2CE\7*\2\2DF\5\16\b\2ED\3\2\2\2EF\3"
+ "\2\2\2FG\3\2\2\2GH\7+\2\2HI\5\30\r\2I\t\3\2\2\2JK\5 \21\2KN\7\64\2\2L"
+ "M\7$\2\2MO\5&\24\2NL\3\2\2\2NO\3\2\2\2O\13\3\2\2\2PQ\5\n\6\2QR\7\'\2\2"
+ "R\r\3\2\2\2ST\5\n\6\2TU\7(\2\2UW\3\2\2\2VS\3\2\2\2WZ\3\2\2\2XV\3\2\2\2"
+ "XY\3\2\2\2Y[\3\2\2\2ZX\3\2\2\2[\\\5\n\6\2\\\17\3\2\2\2]a\7.\2\2^`\5\22"
+ "\n\2_^\3\2\2\2`c\3\2\2\2a_\3\2\2\2ab\3\2\2\2bd\3\2\2\2ca\3\2\2\2de\7/"
+ "\2\2e\21\3\2\2\2fj\5\f\7\2gj\5\24\13\2hj\5\b\5\2if\3\2\2\2ig\3\2\2\2i"
+ "h\3\2\2\2j\23\3\2\2\2kl\7\64\2\2ln\7*\2\2mo\5\16\b\2nm\3\2\2\2no\3\2\2"
+ "\2op\3\2\2\2pq\7+\2\2qr\5\30\r\2r\25\3\2\2\2s}\5\30\r\2t}\5\f\7\2u}\5"
+ "\32\16\2v}\5\34\17\2wx\5&\24\2xy\7\'\2\2y}\3\2\2\2z}\5\36\20\2{}\7\'\2"
+ "\2|s\3\2\2\2|t\3\2\2\2|u\3\2\2\2|v\3\2\2\2|w\3\2\2\2|z\3\2\2\2|{\3\2\2"
+ "\2}\27\3\2\2\2~\u0082\7.\2\2\177\u0081\5\26\f\2\u0080\177\3\2\2\2\u0081"
+ "\u0084\3\2\2\2\u0082\u0080\3\2\2\2\u0082\u0083\3\2\2\2\u0083\u0085\3\2"
+ "\2\2\u0084\u0082\3\2\2\2\u0085\u0086\7/\2\2\u0086\31\3\2\2\2\u0087\u0088"
+ "\7\7\2\2\u0088\u0089\7*\2\2\u0089\u008a\5&\24\2\u008a\u008b\7+\2\2\u008b"
+ "\u008e\5\26\f\2\u008c\u008d\7\b\2\2\u008d\u008f\5\26\f\2\u008e\u008c\3"
+ "\2\2\2\u008e\u008f\3\2\2\2\u008f\33\3\2\2\2\u0090\u0091\7\t\2\2\u0091"
+ "\u0093\7*\2\2\u0092\u0094\5&\24\2\u0093\u0092\3\2\2\2\u0093\u0094\3\2"
+ "\2\2\u0094\u0095\3\2\2\2\u0095\u0097\7\'\2\2\u0096\u0098\5&\24\2\u0097"
+ "\u0096\3\2\2\2\u0097\u0098\3\2\2\2\u0098\u0099\3\2\2\2\u0099\u009b\7\'"
+ "\2\2\u009a\u009c\5&\24\2\u009b\u009a\3\2\2\2\u009b\u009c\3\2\2\2\u009c"
+ "\u009d\3\2\2\2\u009d\u009e\7+\2\2\u009e\u00a6\5\26\f\2\u009f\u00a0\7\n"
+ "\2\2\u00a0\u00a1\7*\2\2\u00a1\u00a2\5&\24\2\u00a2\u00a3\7+\2\2\u00a3\u00a4"
+ "\5\26\f\2\u00a4\u00a6\3\2\2\2\u00a5\u0090\3\2\2\2\u00a5\u009f\3\2\2\2"
+ "\u00a6\35\3\2\2\2\u00a7\u00a9\7\r\2\2\u00a8\u00aa\5&\24\2\u00a9\u00a8"
+ "\3\2\2\2\u00a9\u00aa\3\2\2\2\u00aa\u00ab\3\2\2\2\u00ab\u00b1\7\'\2\2\u00ac"
+ "\u00ad\7\13\2\2\u00ad\u00b1\7\'\2\2\u00ae\u00af\7\f\2\2\u00af\u00b1\7"
+ "\'\2\2\u00b0\u00a7\3\2\2\2\u00b0\u00ac\3\2\2\2\u00b0\u00ae\3\2\2\2\u00b1"
+ "\37\3\2\2\2\u00b2\u00b5\5\"\22\2\u00b3\u00b5\5$\23\2\u00b4\u00b2\3\2\2"
+ "\2\u00b4\u00b3\3\2\2\2\u00b5!\3\2\2\2\u00b6\u00b8\5$\23\2\u00b7\u00b9"
+ "\5,\27\2\u00b8\u00b7\3\2\2\2\u00b9\u00ba\3\2\2\2\u00ba\u00b8\3\2\2\2\u00ba"
+ "\u00bb\3\2\2\2\u00bb#\3\2\2\2\u00bc\u00c2\7\3\2\2\u00bd\u00c2\7\4\2\2"
+ "\u00be\u00c2\7\6\2\2\u00bf\u00c2\7\5\2\2\u00c0\u00c2\7\64\2\2\u00c1\u00bc"
+ "\3\2\2\2\u00c1\u00bd\3\2\2\2\u00c1\u00be\3\2\2\2\u00c1\u00bf\3\2\2\2\u00c1"
+ "\u00c0\3\2\2\2\u00c2%\3\2\2\2\u00c3\u00c4\b\24\1\2\u00c4\u00c5\t\2\2\2"
+ "\u00c5\u00d3\5&\24\24\u00c6\u00c7\t\3\2\2\u00c7\u00d3\5&\24\23\u00c8\u00c9"
+ "\t\4\2\2\u00c9\u00d3\5&\24\22\u00ca\u00cb\7\16\2\2\u00cb\u00d3\5*\26\2"
+ "\u00cc\u00d3\7\64\2\2\u00cd\u00d3\5.\30\2\u00ce\u00cf\7*\2\2\u00cf\u00d0"
+ "\5&\24\2\u00d0\u00d1\7+\2\2\u00d1\u00d3\3\2\2\2\u00d2\u00c3\3\2\2\2\u00d2"
+ "\u00c6\3\2\2\2\u00d2\u00c8\3\2\2\2\u00d2\u00ca\3\2\2\2\u00d2\u00cc\3\2"
+ "\2\2\u00d2\u00cd\3\2\2\2\u00d2\u00ce\3\2\2\2\u00d3\u0107\3\2\2\2\u00d4"
+ "\u00d5\f\20\2\2\u00d5\u00d6\t\5\2\2\u00d6\u0106\5&\24\21\u00d7\u00d8\f"
+ "\17\2\2\u00d8\u00d9\t\3\2\2\u00d9\u0106\5&\24\20\u00da\u00db\f\16\2\2"
+ "\u00db\u00dc\t\6\2\2\u00dc\u0106\5&\24\17\u00dd\u00de\f\r\2\2\u00de\u00df"
+ "\t\7\2\2\u00df\u0106\5&\24\16\u00e0\u00e1\f\f\2\2\u00e1\u00e2\t\b\2\2"
+ "\u00e2\u0106\5&\24\r\u00e3\u00e4\f\13\2\2\u00e4\u00e5\7#\2\2\u00e5\u0106"
+ "\5&\24\f\u00e6\u00e7\f\n\2\2\u00e7\u00e8\7\"\2\2\u00e8\u0106\5&\24\13"
+ "\u00e9\u00ea\f\t\2\2\u00ea\u00eb\7!\2\2\u00eb\u0106\5&\24\n\u00ec\u00ed"
+ "\f\b\2\2\u00ed\u00ee\7\33\2\2\u00ee\u0106\5&\24\t\u00ef\u00f0\f\7\2\2"
+ "\u00f0\u00f1\7\34\2\2\u00f1\u0106\5&\24\b\u00f2\u00f3\f\6\2\2\u00f3\u00f4"
+ "\7$\2\2\u00f4\u0106\5&\24\6\u00f5\u00f6\f\30\2\2\u00f6\u0106\t\2\2\2\u00f7"
+ "\u00f8\f\27\2\2\u00f8\u00fa\7*\2\2\u00f9\u00fb\5(\25\2\u00fa\u00f9\3\2"
+ "\2\2\u00fa\u00fb\3\2\2\2\u00fb\u00fc\3\2\2\2\u00fc\u0106\7+\2\2\u00fd"
+ "\u00fe\f\26\2\2\u00fe\u00ff\7,\2\2\u00ff\u0100\5&\24\2\u0100\u0101\7-"
+ "\2\2\u0101\u0106\3\2\2\2\u0102\u0103\f\25\2\2\u0103\u0104\7)\2\2\u0104"
+ "\u0106\7\64\2\2\u0105\u00d4\3\2\2\2\u0105\u00d7\3\2\2\2\u0105\u00da\3"
+ "\2\2\2\u0105\u00dd\3\2\2\2\u0105\u00e0\3\2\2\2\u0105\u00e3\3\2\2\2\u0105"
+ "\u00e6\3\2\2\2\u0105\u00e9\3\2\2\2\u0105\u00ec\3\2\2\2\u0105\u00ef\3\2"
+ "\2\2\u0105\u00f2\3\2\2\2\u0105\u00f5\3\2\2\2\u0105\u00f7\3\2\2\2\u0105"
+ "\u00fd\3\2\2\2\u0105\u0102\3\2\2\2\u0106\u0109\3\2\2\2\u0107\u0105\3\2"
+ "\2\2\u0107\u0108\3\2\2\2\u0108\'\3\2\2\2\u0109\u0107\3\2\2\2\u010a\u010b"
+ "\5&\24\2\u010b\u010c\7(\2\2\u010c\u010e\3\2\2\2\u010d\u010a\3\2\2\2\u010e"
+ "\u0111\3\2\2\2\u010f\u010d\3\2\2\2\u010f\u0110\3\2\2\2\u0110\u0112\3\2"
+ "\2\2\u0111\u010f\3\2\2\2\u0112\u0113\5&\24\2\u0113)\3\2\2\2\u0114\u0119"
+ "\5$\23\2\u0115\u0116\7,\2\2\u0116\u0117\5&\24\2\u0117\u0118\7-\2\2\u0118"
+ "\u011a\3\2\2\2\u0119\u0115\3\2\2\2\u011a\u011b\3\2\2\2\u011b\u0119\3\2"
+ "\2\2\u011b\u011c\3\2\2\2\u011c\u011e\3\2\2\2\u011d\u011f\5,\27\2\u011e"
+ "\u011d\3\2\2\2\u011f\u0120\3\2\2\2\u0120\u011e\3\2\2\2\u0120\u0121\3\2"
+ "\2\2\u0121\u0126\3\2\2\2\u0122\u0123\7,\2\2\u0123\u0124\5&\24\2\u0124"
+ "\u0125\7-\2\2\u0125\u0127\3\2\2\2\u0126\u0122\3\2\2\2\u0127\u0128\3\2"
+ "\2\2\u0128\u0126\3\2\2\2\u0128\u0129\3\2\2\2\u0129\u0142\3\2\2\2\u012a"
+ "\u012f\5$\23\2\u012b\u012c\7,\2\2\u012c\u012d\5&\24\2\u012d\u012e\7-\2"
+ "\2\u012e\u0130\3\2\2\2\u012f\u012b\3\2\2\2\u0130\u0131\3\2\2\2\u0131\u012f"
+ "\3\2\2\2\u0131\u0132\3\2\2\2\u0132\u0136\3\2\2\2\u0133\u0135\5,\27\2\u0134"
+ "\u0133\3\2\2\2\u0135\u0138\3\2\2\2\u0136\u0134\3\2\2\2\u0136\u0137\3\2"
+ "\2\2\u0137\u0142\3\2\2\2\u0138\u0136\3\2\2\2\u0139\u013f\5$\23\2\u013a"
+ "\u013c\7*\2\2\u013b\u013d\5(\25\2\u013c\u013b\3\2\2\2\u013c\u013d\3\2"
+ "\2\2\u013d\u013e\3\2\2\2\u013e\u0140\7+\2\2\u013f\u013a\3\2\2\2\u013f"
+ "\u0140\3\2\2\2\u0140\u0142\3\2\2\2\u0141\u0114\3\2\2\2\u0141\u012a\3\2"
+ "\2\2\u0141\u0139\3\2\2\2\u0142+\3\2\2\2\u0143\u0144\7,\2\2\u0144\u0145"
+ "\7-\2\2\u0145-\3\2\2\2\u0146\u014b\7\60\2\2\u0147\u014b\7\61\2\2\u0148"
+ "\u014b\7\62\2\2\u0149\u014b\7\63\2\2\u014a\u0146\3\2\2\2\u014a\u0147\3"
+ "\2\2\2\u014a\u0148\3\2\2\2\u014a\u0149\3\2\2\2\u014b/\3\2\2\2$\63;ENX"
+ "ain|\u0082\u008e\u0093\u0097\u009b\u00a5\u00a9\u00b0\u00b4\u00ba\u00c1"
+ "\u00d2\u00fa\u0105\u0107\u010f\u011b\u0120\u0128\u0131\u0136\u013c\u013f"
+ "\u0141\u014a";
public static final ATN _ATN = new ATNDeserializer().deserialize(_serializedATN.toCharArray());
static {
_decisionToDFA = new DFA[_ATN.getNumberOfDecisions()];
for (int i = 0; i < _ATN.getNumberOfDecisions(); i++) {
_decisionToDFA[i] = new DFA(_ATN.getDecisionState(i), i);
}
}
}
|
guanlichang/novel | src/main/java/org/yidu/novel/filter/GzipFilter.java | <gh_stars>0
package org.yidu.novel.filter;
import java.io.IOException;
import javax.servlet.Filter;
import javax.servlet.FilterChain;
import javax.servlet.FilterConfig;
import javax.servlet.ServletException;
import javax.servlet.ServletRequest;
import javax.servlet.ServletResponse;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.yidu.novel.constant.YiDuConfig;
import org.yidu.novel.constant.YiDuConstants;
/**
*
* <p>
* Gzip过滤器
* </p>
* Copyright(c) 2014 YiDu-Novel. All rights reserved.
*
* @version 1.0.0
* @author shinpa.you
*/
public class GzipFilter implements Filter {
/**
* 过滤器配置
*/
private FilterConfig filterConfig = null;
/**
* 构造方法
*
* @return 过滤器配置
*/
protected final FilterConfig getFilterConfig() {
return this.filterConfig;
}
/**
* {@inheritDoc}
*
* @see javax.servlet.Filter#init(javax.servlet.FilterConfig)
*/
@Override
public void init(final FilterConfig filterConfig) throws ServletException {
this.filterConfig = filterConfig;
}
/**
* {@inheritDoc}
*
* @see javax.servlet.Filter#destroy()
*/
@Override
public void destroy() {
this.filterConfig = null;
}
@Override
public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException,
ServletException {
if (!YiDuConstants.yiduConf.getBoolean(YiDuConfig.GZIP_EFFECTIVE, false)) {
chain.doFilter(req, res);
} else {
if (req instanceof HttpServletRequest) {
if (!((HttpServletRequest) req).getRequestURI().startsWith("/download")) {
// download以外的请求做Gzip处理
HttpServletRequest request = (HttpServletRequest) req;
HttpServletResponse response = (HttpServletResponse) res;
String ae = request.getHeader("accept-encoding");
if (ae != null && ae.indexOf("gzip") != -1) {
GZIPResponseWrapper wrappedResponse = new GZIPResponseWrapper(response);
chain.doFilter(req, wrappedResponse);
wrappedResponse.finishResponse();
return;
}
}
}
chain.doFilter(req, res);
}
}
}
|
LarryHsiao/Clotho | src/main/java/com/larryhsiao/clotho/date/DateEndCalendar.java | <reponame>LarryHsiao/Clotho
package com.larryhsiao.clotho.date;
import com.larryhsiao.clotho.Source;
import java.util.Calendar;
/**
* Source to generate Calendar which time is 23:59 of the given timestamp.
*/
public class DateEndCalendar implements Source<Calendar> {
private final long millis;
private final Calendar calendar;
public DateEndCalendar(long millis) {
this(millis, Calendar.getInstance());
}
public DateEndCalendar(long millis, Calendar calendar) {
this.millis = millis;
this.calendar = calendar;
}
@Override
public Calendar value() {
calendar.setTimeInMillis(millis);
calendar.set(Calendar.HOUR_OF_DAY, 23);
calendar.set(Calendar.MINUTE, 59);
calendar.set(Calendar.SECOND, 59);
calendar.set(Calendar.MILLISECOND, 999);
return calendar;
}
}
|
sw402f19/Ardu3K | src/exception/factory/SemanticException.java | package exception.factory;
public abstract class SemanticException extends RuntimeException {
public SemanticException() {
}
public SemanticException(String message) {
super(message);
}
public SemanticException(Throwable cause) {
super(cause.getMessage(), cause);
}
}
|
jimmyblylee/XXMPS | src/apms-serv/src/main/java/com/founder/bj/apms/auxpolice/entity/AuxWork.java | /* ***************************************************************************
* EZ.JWAF/EZ.JCWAP: Easy series Production.
* Including JWAF(Java-based Web Application Framework)
* and JCWAP(Java-based Customized Web Application Platform).
* Copyright (C) 2016-2017 the original author or authors.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of MIT License as published by
* the Free Software Foundation;
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
* See the MIT License for more details.
*
* You should have received a copy of the MIT License along
* with this library; if not, write to the Free Software Foundation.
* ***************************************************************************/
package com.founder.bj.apms.auxpolice.entity;
import javax.persistence.*;
import org.hibernate.annotations.GenericGenerator;
import com.founder.bj.apms.sys.entity.SysUser;
/**
* Description: Aux Work Entity.<br>
* Created by <NAME> on 2017/10/9.
*
* @author <NAME>
*/
@Entity
@Table(name = "APMS_AUX_WORK")
@SuppressWarnings("unused")
public class AuxWork implements AuxStuff {
private static final long serialVersionUID = 3938721311908893826L;
/** Id. */
@Id
@Column(name = "WORK_ID")
@GeneratedValue(generator = "apms_uuid")
@GenericGenerator(name = "apms_uuid", strategy = "uuid2")
private String id;
/** Work for department name. */
@Column(name = "WORK_DEPT")
private String dept;
/** Job title. */
@Column(name = "WORK_JOB")
private String job;
/** Start date. */
@OrderBy
@Column(name = "WORK_START")
private String start;
/** End date. */
@Column(name = "WORK_END")
private String end;
/** 最近更新人ID与用户表关联. */
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "LATEST_UPDATE_USER")
private SysUser lastUpdateUser;
/** 最近更新时间. */
@Column(name = "LATEST_UPDATE_DATE")
private String lastUpdateDate;
/** 最近更新IP. */
@Column(name = "LATEST_UPDATE_IP")
private String lastUpdateIp;
/** Aux. */
@ManyToOne
@JoinColumn(name = "AUX_ID")
private AuxInfo aux;
/**
* Get the id.
*
* @return return the id
*/
public String getId() {
return id;
}
/**
* Set id.
*
* @param id the id to set
*/
public void setId(String id) {
this.id = id;
}
/**
* Get the dept.
*
* @return return the dept
*/
public String getDept() {
return dept;
}
/**
* Set dept.
*
* @param dept the dept to set
*/
public void setDept(String dept) {
this.dept = dept;
}
/**
* Get the job.
*
* @return return the job
*/
public String getJob() {
return job;
}
/**
* Set job.
*
* @param job the job to set
*/
public void setJob(String job) {
this.job = job;
}
/**
* Get the start.
*
* @return return the start
*/
public String getStart() {
return start;
}
/**
* Set start.
*
* @param start the start to set
*/
public void setStart(String start) {
this.start = start;
}
/**
* Get the end.
*
* @return return the end
*/
public String getEnd() {
return end;
}
/**
* Set end.
*
* @param end the end to set
*/
public void setEnd(String end) {
this.end = end;
}
/**
* Get the lastUpdateUser.
*
* @return return the lastUpdateUser
*/
public SysUser getLastUpdateUser() {
return lastUpdateUser;
}
/**
* Set lastUpdateUser.
*
* @param lastUpdateUser the lastUpdateUser to set
*/
public void setLastUpdateUser(SysUser lastUpdateUser) {
this.lastUpdateUser = lastUpdateUser;
}
/**
* Get the lastUpdateDate.
*
* @return return the lastUpdateDate
*/
public String getLastUpdateDate() {
return lastUpdateDate;
}
/**
* Set lastUpdateDate.
*
* @param lastUpdateDate the lastUpdateDate to set
*/
public void setLastUpdateDate(String lastUpdateDate) {
this.lastUpdateDate = lastUpdateDate;
}
/**
* Get the lastUpdateIp.
*
* @return return the lastUpdateIp
*/
public String getLastUpdateIp() {
return lastUpdateIp;
}
/**
* Set lastUpdateIp.
*
* @param lastUpdateIp the lastUpdateIp to set
*/
public void setLastUpdateIp(String lastUpdateIp) {
this.lastUpdateIp = lastUpdateIp;
}
/**
* Get the aux.
*
* @return return the aux
*/
public AuxInfo getAux() {
return aux;
}
/**
* Set aux.
*
* @param aux the aux to set
*/
public void setAux(AuxInfo aux) {
this.aux = aux;
}
}
|
ravikant7890/GoFFish_Giraph | giraph-block-app/src/main/java/org/apache/giraph/block_app/framework/piece/DefaultParentPiece.java | <reponame>ravikant7890/GoFFish_Giraph<gh_stars>1-10
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.giraph.block_app.framework.piece;
import org.apache.giraph.block_app.framework.api.BlockMasterApi;
import org.apache.giraph.block_app.framework.api.BlockWorkerSendApi;
import org.apache.giraph.block_app.framework.api.CreateReducersApi;
import org.apache.giraph.block_app.framework.piece.global_comm.ReduceUtilsObject;
import org.apache.giraph.block_app.framework.piece.global_comm.ReducerHandle;
import org.apache.giraph.block_app.framework.piece.global_comm.internal.CreateReducersApiWrapper;
import org.apache.giraph.block_app.framework.piece.global_comm.internal.ReducersForPieceHandler;
import org.apache.giraph.block_app.framework.piece.interfaces.VertexPostprocessor;
import org.apache.giraph.block_app.framework.piece.interfaces.VertexSender;
import org.apache.giraph.block_app.framework.piece.messages.ObjectMessageClasses;
import org.apache.giraph.block_app.framework.piece.messages.SupplierFromConf;
import org.apache.giraph.block_app.framework.piece.messages.SupplierFromConf.DefaultMessageFactorySupplierFromConf;
import org.apache.giraph.block_app.framework.piece.messages.SupplierFromConf.SupplierFromConfByCopy;
import org.apache.giraph.combiner.MessageCombiner;
import org.apache.giraph.comm.messages.MessageEncodeAndStoreType;
import org.apache.giraph.conf.EnumConfOption;
import org.apache.giraph.conf.GiraphConfigurationSettable;
import org.apache.giraph.conf.GiraphConstants;
import org.apache.giraph.conf.ImmutableClassesGiraphConfiguration;
import org.apache.giraph.conf.MessageClasses;
import org.apache.giraph.factories.MessageValueFactory;
import org.apache.giraph.graph.Vertex;
import org.apache.giraph.types.NoMessage;
import org.apache.hadoop.io.DoubleWritable;
import org.apache.hadoop.io.FloatWritable;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Writable;
import org.apache.hadoop.io.WritableComparable;
import com.google.common.base.Preconditions;
/**
* Additional abstract implementations for all pieces to be used.
* Code here is not in AbstractPiece only to allow for non-standard
* non-user-defined pieces. <br>
* Only logic used by the underlying framework directly is in AbstractPiece
* itself.
*
* @param <I> Vertex id type
* @param <V> Vertex value type
* @param <E> Edge value type
* @param <M> Message type
* @param <WV> Worker value type
* @param <WM> Worker message type
* @param <S> Execution stage type
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
public abstract class DefaultParentPiece<I extends WritableComparable,
V extends Writable, E extends Writable, M extends Writable, WV,
WM extends Writable, S> extends AbstractPiece<I, V, E, M, WV, WM, S> {
// TODO move to GiraphConstants
/**
* This option will tell which message encode & store enum to force, when
* combining is not enabled.
*
* MESSAGE_ENCODE_AND_STORE_TYPE and this property are basically upper
* and lower bound on message store type, when looking them in order from
* not doing anything special, to most advanced type:
* BYTEARRAY_PER_PARTITION,
* EXTRACT_BYTEARRAY_PER_PARTITION,
* POINTER_LIST_PER_VERTEX
* resulting encode type is going to be:
* pieceEncodingType = piece.allowOneMessageToManyIdsEncoding() ?
* POINTER_LIST_PER_VERTEX : BYTEARRAY_PER_PARTITION)
* Math.max(index(minForce), Math.min(index(maxAllowed), index(pieceType);
*
* This is useful to force all pieces onto particular message store, even
* if they do not overrideallowOneMessageToManyIdsEncoding, though that might
* be rarely needed.
* This option might be more useful for fully local computation,
* where overall job behavior is quite different.
*/
public static final EnumConfOption<MessageEncodeAndStoreType>
MESSAGE_ENCODE_AND_STORE_TYPE_MIN_FORCE =
EnumConfOption.create("giraph.messageEncodeAndStoreTypeMinForce",
MessageEncodeAndStoreType.class,
MessageEncodeAndStoreType.BYTEARRAY_PER_PARTITION,
"Select the message_encode_and_store_type min force to use");
private final ReduceUtilsObject reduceUtils = new ReduceUtilsObject();
private ReducersForPieceHandler reducersHandler;
// Overridable functions
/**
* Override to register any potential reducers used by this piece,
* through calls to {@code reduceApi}, which will return reducer handles
* for simple.
* <br/>
* Tip: Without defining a field, first write here name of the field and what
* you want to reduce, like:
* <br/>
* {@code totalSum = reduceApi.createLocalReducer(SumReduce.DOUBLE); }
* <br/>
* and then use tools your IDE provides to generate field signature itself,
* which might be slightly complex:
* <br/>
* {@code ReducerHandle<DoubleWritable, DoubleWritable> totalSum; }
*/
public void registerReducers(CreateReducersApi reduceApi, S executionStage) {
}
/**
* Override to do vertex send processing.
*
* Creates handler that defines what should be executed on worker
* during send phase.
*
* This logic gets executed first.
* This function is called once on each worker on each thread, in parallel,
* on their copy of Piece object to create functions handler.
*
* If returned object implements Postprocessor interface, then corresponding
* postprocess() function is going to be called once, after all vertices
* corresponding thread needed to process are done.
*/
public VertexSender<I, V, E> getVertexSender(
BlockWorkerSendApi<I, V, E, M> workerApi, S executionStage) {
return null;
}
/**
* Override to specify type of the message this Piece sends, if it does
* send messages.
*
* If not overwritten, no messages can be sent.
*/
protected Class<M> getMessageClass() {
return null;
}
/**
* Override to specify message value factory to be used,
* which creates objects into which messages will be deserialized.
*
* If not overwritten, or null is returned, DefaultMessageValueFactory
* will be used.
*/
protected MessageValueFactory<M> getMessageFactory(
ImmutableClassesGiraphConfiguration conf) {
return null;
}
/**
* Override to specify message combiner to be used, if any.
*
* Message combiner itself should be immutable
* (i.e. it will be call simultanously from multiple threads)
*/
protected MessageCombiner<? super I, M> getMessageCombiner(
ImmutableClassesGiraphConfiguration conf) {
return null;
}
/**
* Override to specify that this Piece allows one to many ids encoding to be
* used for messages.
* You should override this function, if you are sending identical message to
* all targets, and message itself is not extremely small.
*/
protected boolean allowOneMessageToManyIdsEncoding() {
return false;
}
@Override
public MessageClasses<I, M> getMessageClasses(
ImmutableClassesGiraphConfiguration conf) {
Class<M> messageClass = null;
MessageValueFactory<M> messageFactory = getMessageFactory(conf);
MessageCombiner<? super I, M> messageCombiner = getMessageCombiner(conf);
if (messageFactory != null) {
messageClass = (Class) messageFactory.newInstance().getClass();
} else if (messageCombiner != null) {
messageClass = (Class) messageCombiner.createInitialMessage().getClass();
}
if (messageClass != null) {
Preconditions.checkState(getMessageClass() == null,
"Piece %s defines getMessageFactory or getMessageCombiner, " +
"so it doesn't need to define getMessageClass.",
toString());
} else {
messageClass = getMessageClass();
if (messageClass == null) {
messageClass = (Class) NoMessage.class;
}
}
SupplierFromConf<MessageValueFactory<M>> messageFactorySupplier;
if (messageFactory != null) {
messageFactorySupplier =
new SupplierFromConfByCopy<MessageValueFactory<M>>(messageFactory);
} else {
messageFactorySupplier =
new DefaultMessageFactorySupplierFromConf<>(messageClass);
}
SupplierFromConf<? extends MessageCombiner<? super I, M>>
messageCombinerSupplier;
if (messageCombiner != null) {
messageCombinerSupplier = new SupplierFromConfByCopy<>(messageCombiner);
} else {
messageCombinerSupplier = null;
}
int maxAllowed =
GiraphConstants.MESSAGE_ENCODE_AND_STORE_TYPE.get(conf).ordinal();
int minForce = MESSAGE_ENCODE_AND_STORE_TYPE_MIN_FORCE.get(conf).ordinal();
Preconditions.checkState(maxAllowed >= minForce);
int pieceEncodeType = (allowOneMessageToManyIdsEncoding() ?
MessageEncodeAndStoreType.POINTER_LIST_PER_VERTEX :
MessageEncodeAndStoreType.BYTEARRAY_PER_PARTITION).ordinal();
// bound piece type with boundaries:
pieceEncodeType = Math.max(minForce, Math.min(maxAllowed, pieceEncodeType));
MessageEncodeAndStoreType messageEncodeAndStoreType =
MessageEncodeAndStoreType.values()[pieceEncodeType];
if (messageFactory instanceof GiraphConfigurationSettable) {
throw new IllegalStateException(
messageFactory.getClass() + " MessageFactory in " + this +
" Piece implements GiraphConfigurationSettable");
}
if (messageCombiner instanceof GiraphConfigurationSettable) {
throw new IllegalStateException(
messageCombiner.getClass() + " MessageCombiner in " + this +
" Piece implements GiraphConfigurationSettable");
}
return new ObjectMessageClasses<>(
messageClass, messageFactorySupplier,
messageCombinerSupplier, messageEncodeAndStoreType);
}
// Internal implementation
@Override
public final InnerVertexSender getWrappedVertexSender(
final BlockWorkerSendApi<I, V, E, M> workerApi, S executionStage) {
reducersHandler.vertexSenderWorkerPreprocess(workerApi);
final VertexSender<I, V, E> functions =
getVertexSender(workerApi, executionStage);
return new InnerVertexSender() {
@Override
public void vertexSend(Vertex<I, V, E> vertex) {
if (functions != null) {
functions.vertexSend(vertex);
}
}
@Override
public void postprocess() {
if (functions instanceof VertexPostprocessor) {
((VertexPostprocessor) functions).postprocess();
}
reducersHandler.vertexSenderWorkerPostprocess(workerApi);
}
};
}
@Override
public final void wrappedRegisterReducers(
BlockMasterApi masterApi, S executionStage) {
reducersHandler = new ReducersForPieceHandler();
registerReducers(new CreateReducersApiWrapper(
masterApi, reducersHandler), executionStage);
}
// utility functions:
// TODO Java8 - move these as default functions to VertexSender interface
protected final void reduceDouble(
ReducerHandle<DoubleWritable, ?> reduceHandle, double value) {
reduceUtils.reduceDouble(reduceHandle, value);
}
protected final void reduceFloat(
ReducerHandle<FloatWritable, ?> reduceHandle, float value) {
reduceUtils.reduceFloat(reduceHandle, value);
}
protected final void reduceLong(
ReducerHandle<LongWritable, ?> reduceHandle, long value) {
reduceUtils.reduceLong(reduceHandle, value);
}
protected final void reduceInt(
ReducerHandle<IntWritable, ?> reduceHandle, int value) {
reduceUtils.reduceInt(reduceHandle, value);
}
}
|
svendcsvendsen/judoassistant | src/ui/widgets/judoassistant_preferences_dialog.cpp | <reponame>svendcsvendsen/judoassistant<gh_stars>1-10
#include <QDialogButtonBox>
#include <QVBoxLayout>
#include <QHBoxLayout>
#include <QStackedWidget>
#include <QListWidget>
#include <QTableView>
#include "ui/widgets/judoassistant_preferences_dialog.hpp"
#include "ui/widgets/web_connection_preferences_widget.hpp"
#include "ui/widgets/save_preferences_widget.hpp"
JudoassistantPreferencesDialog::JudoassistantPreferencesDialog(MasterStoreManager & storeManager, QWidget *parent)
: QDialog(parent)
, mStoreManager(storeManager)
{
QStackedWidget *stackedWidget = new QStackedWidget;
QListWidget *listWidget = new QListWidget;
listWidget->setMaximumWidth(150);
// Add save preferences
{
QWidget *widget = new SavePreferencesWidget(storeManager);
listWidget->addItem(tr("Tournament File Saving"));
stackedWidget->addWidget(widget);
}
// Add web connection page
{
QWidget *widget = new WebConnectionPreferencesWidget(storeManager);
listWidget->addItem(tr("Web Connection"));
stackedWidget->addWidget(widget);
}
listWidget->setCurrentRow(0);
stackedWidget->setCurrentIndex(0);
connect(listWidget, &QListWidget::currentRowChanged, stackedWidget, &QStackedWidget::setCurrentIndex);
// Setup layouts
QVBoxLayout *mainLayout = new QVBoxLayout;
QHBoxLayout *horizontalLayout = new QHBoxLayout;
horizontalLayout->addWidget(listWidget);
horizontalLayout->addWidget(stackedWidget);
mainLayout->addLayout(horizontalLayout);
// Setup button box
{
QDialogButtonBox *buttonBox = new QDialogButtonBox;
buttonBox->addButton(tr("Close"), QDialogButtonBox::AcceptRole);
mainLayout->addWidget(buttonBox);
connect(buttonBox, &QDialogButtonBox::accepted, this, &JudoassistantPreferencesDialog::closeClick);
}
setLayout(mainLayout);
setWindowTitle(tr("JudoAssistant Preferences"));
setGeometry(geometry().x(), geometry().y(), 800, 400);
}
void JudoassistantPreferencesDialog::closeClick() {
accept();
}
|
camshaft/postcss-runtime | src/compiler/process/color.js | import parser from 'postcss-values-parser';
import Color from 'color';
const colorMod = process.env.POSTCSS_RUNTIME_PATH || 'postcss-runtime';
/**
* color: color(red shade(20%));
*/
export default function plugin(root, compilation) {
root.walkDecls((rule) => {
const value = rule.value;
if (!value) return;
value.walk((node) => {
if (node.type === 'func' && (node.value === 'color' || node.value === 'color-mod')) {
parseColor(node, compilation);
}
});
});
}
function parseColor(fun, compilation) {
fun.value = compilation.import(colorMod, 'applyColorMods');
fun.unquote = true;
const args = cleanArgs(fun);
fun.removeAll();
args.forEach((arg, i) => {
if (i === 0) {
const value = color(arg, compilation);
if (!value) {
throw new Error(`Invalid color value: ${String(arg)}`);
}
fun.append(value);
return;
}
const value = adjusters(arg, compilation);
if (value) {
fun.append(value);
return;
}
// TODO use postcss warnings
console.error(`Invalid adjuster function: ${arg.toString()}`);
return false;
});
}
const rgba = choice(['red', 'green', 'blue', 'alpha', 'a'], (value) => {
return value === 'a' ?
'alpha' :
value;
});
const hue = choice(['hue', 'h'], () => 'hue');
const saturation = choice(['saturation', 's'], () => 'saturation');
const lightness = choice(['lightness', 's'], () => 'lightness');
const whiteness = choice(['whiteness', 's'], () => 'whiteness');
const blackness = choice(['blackness', 's'], () => 'blackness');
const rgb = toCombinator('rgb');
const PLUS = operator('+');
const MINUS = operator('-');
const MULT = operator('*');
const colorSpaces = choice(['rgb', 'hsl', 'hwb']);
const ops = {
'+': 'add',
'-': 'sub',
'*': 'mult',
};
const number = numberComb('parseNumber', '', (node, compilation) => {
node.unquote = true;
});
const percentage = numberComb('parsePercentage', '%', (node, compilation) => {
return callNumberFunction(node, compilation, 'percentage');
});
const angle = numberComb('parseAngle', ['', 'deg', 'grad', 'rad', 'turn'], (node, compilation) => {
const unit = node.unit || 'deg';
return callNumberFunction(node, compilation, unit);
});
const adjusters = choice([
func(rgba, [
option(choice([PLUS, MINUS, MULT])),
choice([number, percentage]),
], (node, compilation, args) => {
let name = node.value;
const op = args[0];
if (op) {
op.value = compilation.import(colorMod, ops[op.value]);
op.unquote = true;
} else {
args[0] = parser.word({
value: compilation.import(colorMod, 'set'),
unquote: true,
});
}
node.value = compilation.import(colorMod, name);
node.unquote = true;
node.nodes = args;
}),
func(rgb, [
choice([PLUS, MINUS]),
option(choice([number, percentage])),
option(choice([number, percentage])),
option(choice([number, percentage])),
], (node, compilation, args) => {
let name = node.value;
const op = args[0];
op.value = compilation.import(colorMod, ops[op.value]);
op.unquote = true;
node.value = compilation.import(colorMod, name);
node.unquote = true;
node.nodes = args;
}),
func(rgb, [
choice([PLUS, MINUS]),
// hashToken, // TODO
], (node, compilation, args) => {
// TODO
}),
func(rgb, [
MULT,
percentage
], (node, compilation, args) => {
const name = node.value + 'Mult';
node.value = compilation.import(colorMod, name);
node.unquote = true;
node.nodes = args.slice(1);
}),
func(hue, [
option(choice([PLUS, MINUS, MULT])),
angle,
], hsl),
func(saturation, [
option(choice([PLUS, MINUS, MULT])),
option(choice([number, percentage])),
], hsl),
func(lightness, [
option(choice([PLUS, MINUS, MULT])),
option(choice([number, percentage])),
], hsl),
func(whiteness, [
option(choice([PLUS, MINUS, MULT])),
option(choice([number, percentage])),
], hsl),
func(blackness, [
option(choice([PLUS, MINUS, MULT])),
option(choice([number, percentage])),
], hsl),
func('tint', [
percentage,
], tintShade),
func('shade', [
percentage,
], tintShade),
func('blend', [
color,
percentage,
option(colorSpaces),
], blend),
func('blenda', [
color,
percentage,
option(colorSpaces),
], blend),
func('contrast', [
option(percentage),
], contrast),
]);
function cleanArgs(fun) {
const args = [];
fun.each((arg, i) => {
const type = arg.type;
if (type === 'string') {
throw new Error(`Invalid color-mod argument: ${String(arg)}`);
}
if (type === 'func' ||
type === 'number' ||
type === 'operator' ||
type === 'word') return args.push(arg.clone());
});
return args;
}
function isVariable(node) {
return node && node.type === 'function' && node.value === 'var';
}
function toCombinator(value) {
if (typeof value === 'function') return value;
return (v) => v === value && value;
}
function choice(choices, transform = (v) => v) {
choices = choices.map(toCombinator);
return (value, compilation) => {
for (let i = 0; i < choices.length; i++) {
const res = choices[i](value, compilation);
if (res) return (transform(res, compilation) || res);
}
return false;
};
}
function word(name) {
return (node) => {
return node.type === 'word' && node.value === name && node;
};
}
function operator(name) {
return (node) => {
return node.type === 'operator' && node.value === name && node;
};
}
function func(name, argMatchers, transform = v => v) {
name = toCombinator(name);
argMatchers = argMatchers.map(toCombinator);
return (node, compilation) => {
if (!node || node.type !== 'func') return false;
const value = name(node.value, compilation);
if (!value) return false;
node.value = value;
const args = cleanArgs(node);
let j = 0;
const out = [];
for (let i = 0; i < argMatchers.length; i++) {
let res = argMatchers[i](args[j], compilation);
if (!res) return false;
if (res === option) {
res = undefined;
} else {
j++;
}
out[i] = res;
}
node.removeAll();
out.forEach(arg => arg && node.append(arg));
return (transform(node, compilation, out) || node);
};
}
function option(fun) {
return (node, compilation) => {
if (!node) return option;
const value = fun(node, compilation);
if (!value) return option;
return value;
};
}
function color(node, compilation) {
const type = node.type;
const value = node.value;
if (type === 'func') {
switch(value) {
case 'color':
case 'color-mod':
return node;
case 'var':
return callNumberFunction(node, compilation, 'applyColorMods', false);
case 'rgb':
case 'rgba':
case 'hsl':
case 'hsla':
case 'hsv':
case 'hwb':
case 'hcg':
case 'cmyk':
case 'xyz':
case 'lab':
// TODO convert into color([a, b, c], model)
return callNumberFunction(node, compilation, 'applyColorMods', false);
default:
return false;
}
}
if (type === 'word') {
if (value === 'currentColor') return false;
try {
new Color(value);
} catch (e) {
return false;
}
return callNumberFunction(node, compilation, 'applyColorMods', false);
}
return false;
}
function callNumberFunction(node, compilation, name, unquote = true) {
const call = parser.func({
unquote: true,
value: compilation.import(colorMod, name),
source: node.source,
sourceIndex: node.sourceIndex,
});
call.append(node.clone({
unquote: unquote,
unit: '',
}));
return call;
}
function numberComb(parser, unit = '', transform = v => v) {
if (!Array.isArray(unit)) unit = [unit]
return (node, compilation) => {
if (isVariable(node)) {
return callNumberFunction(node, compilation, parser);
}
return node &&
node.type === 'number' &&
~unit.indexOf(node.unit) &&
(transform(node, compilation) || node);
};
}
function hsl(node, compilation, args) {
let name = node.value;
const op = args[0];
if (op) {
op.value = compilation.import(colorMod, ops[op.value]);
op.unquote = true;
} else {
args[0] = parser.word({
value: compilation.import(colorMod, 'set'),
unquote: true,
});
}
node.value = compilation.import(colorMod, name);
node.unquote = true;
node.nodes = args;
};
function tintShade(node, compilation, args) {
node.value = compilation.import(colorMod, node.value);
node.unquote = true;
}
function blend(node, compilation, args) {
node.value = compilation.import(colorMod, node.value);
node.unquote = true;
}
function contrast(node, compilation, args) {
node.value = compilation.import(colorMod, node.value);
node.unquote = true;
}
|
bangchuanliu/algorithm-examples | leetcode/src/main/java/common/QuickSort.java | package common;
public class QuickSort {
public void sort(int[] A) {
if (A == null || A.length == 0) {
return;
}
qSort(A, 0, A.length - 1);
}
public int partition(int[] A, int low, int high) {
int r = A[high];
int i = low - 1;
int j = low;
while (j < high) {
if (A[j] <= r) {
i++;
swap(A, i, j);
}
j++;
}
i++;
swap(A, i, high);
return i;
}
public void swap(int[] A, int i, int j) {
int temp = A[i];
A[i] = A[j];
A[j] = temp;
}
public void qSort(int[] A, int low, int high) {
if (low < high) {
int r = partition(A, low, high);
qSort(A, low, r - 1);
qSort(A, r + 1, high);
}
}
public static void main(String[] args){
int[] A= {1,3,5,9,2,4,1,5,7};
new QuickSort().sort(A);
for(int a : A){
System.out.print(a + " ");
}
}
}
|
maddy-torqata/gokul-organics1 | node_modules/@fortawesome/pro-solid-svg-icons/faMistletoe.js | 'use strict';
Object.defineProperty(exports, '__esModule', { value: true });
var prefix = 'fas';
var iconName = 'mistletoe';
var width = 576;
var height = 512;
var ligatures = [];
var unicode = 'f7b4';
var svgPathData = 'M373.3 117.3c23.6 0 42.7-19.1 42.7-42.7S396.9 32 373.3 32s-42.7 19.1-42.7 42.7 19.2 42.6 42.7 42.6zm168.8 144.1c-26-26-89.6-38.6-130.9-44.2L312 117.1c-8.4-12.1-13.3-26.6-13.3-42.4s5-30.3 13.3-42.4V16c0-8.8-7.2-16-16-16h-16c-8.8 0-16 7.2-16 16v102.1l-99.1 99.1C123.6 222.8 60 235.4 34 261.4c-40 40-45.4 99.4-12.1 132.7 33.3 33.3 92.8 27.9 132.7-12.1 11.4-11.4 20.1-30.2 26.9-51 6.8 12.3 19.5 20.9 34.5 20.9 22.1 0 40-17.9 40-40s-17.9-40-40-40c-8.2 0-15.4 3.1-21.7 7.3 1.8-10 3.4-19.6 4.5-28.2l65.2-65.2v72.8c14.6 13.2 24 32.1 24 53.3 0 39.7-32.3 72-72 72-6.2 0-12.1-1-17.8-2.5-3.7 9.9-6.2 19.5-6.2 28.1 0 56.6 43 102.4 96 102.4s96-45.8 96-102.4c0-38.1-43.6-94.6-72-127.3v-96.3l65.2 65.2c5.6 41.3 18.2 104.9 44.2 130.9 40 40 99.4 45.4 132.7 12.1 33.4-33.3 28-92.7-12-132.7z';
exports.definition = {
prefix: prefix,
iconName: iconName,
icon: [
width,
height,
ligatures,
unicode,
svgPathData
]};
exports.faMistletoe = exports.definition;
exports.prefix = prefix;
exports.iconName = iconName;
exports.width = width;
exports.height = height;
exports.ligatures = ligatures;
exports.unicode = unicode;
exports.svgPathData = svgPathData; |
gatordevin/BoofCV | main/boofcv-recognition/src/main/java/boofcv/deepboof/BaseImageClassifier.java | /*
* Copyright (c) 2020, <NAME>. All Rights Reserved.
*
* This file is part of BoofCV (http://boofcv.org).
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package boofcv.deepboof;
import boofcv.abst.scene.ImageClassifier;
import boofcv.struct.image.GrayF32;
import boofcv.struct.image.ImageType;
import boofcv.struct.image.Planar;
import deepboof.Function;
import deepboof.graph.FunctionSequence;
import deepboof.tensors.Tensor_F32;
import org.ddogleg.struct.DogArray;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
/**
* Base class for ImageClassifiers which implements common elements
*
* @author <NAME>
*/
public abstract class BaseImageClassifier implements ImageClassifier<Planar<GrayF32>> {
protected FunctionSequence<Tensor_F32, Function<Tensor_F32>> network;
// List of all the categories
protected List<String> categories = new ArrayList<>();
protected ImageType<Planar<GrayF32>> imageType = ImageType.pl(3, GrayF32.class);
// Resizes input image for the network
protected ClipAndReduce<Planar<GrayF32>> massage = new ClipAndReduce<>(true, imageType);
// size of square image
protected int imageSize;
// Input image adjusted to network input size
protected Planar<GrayF32> imageRgb;
// Storage for the tensor into the image
protected Tensor_F32 tensorInput;
protected Tensor_F32 tensorOutput;
// storage for the final output
protected DogArray<Score> categoryScores = new DogArray<>(Score::new);
protected int categoryBest;
Comparator<Score> comparator = ( o1, o2 ) -> {
if (o1.score < o2.score)
return 1;
else if (o1.score > o2.score)
return -1;
else
return 0;
};
protected BaseImageClassifier( int imageSize ) {
this.imageSize = imageSize;
imageRgb = new Planar<>(GrayF32.class, imageSize, imageSize, 3);
tensorInput = new Tensor_F32(1, 3, imageSize, imageSize);
}
@Override
public ImageType<Planar<GrayF32>> getInputType() {
return imageType;
}
/**
* The original implementation takes in an image then crops it randomly. This is primarily for training but is
* replicated here to reduce the number of differences
*
* @param image Image being processed. Must be RGB image. Pixel values must have values from 0 to 255.
*/
@Override
public void classify( Planar<GrayF32> image ) {
DataManipulationOps.imageToTensor(preprocess(image), tensorInput, 0);
innerProcess(tensorInput);
}
/**
* Massage the input image into a format recognized by the network
*/
protected Planar<GrayF32> preprocess( Planar<GrayF32> image ) {
// Shrink the image to input size
if (image.width == imageSize && image.height == imageSize) {
this.imageRgb.setTo(image);
} else if (image.width < imageSize || image.height < imageSize) {
throw new IllegalArgumentException("Image width or height is too small");
} else {
massage.massage(image, imageRgb);
}
return imageRgb;
}
protected void innerProcess( Tensor_F32 tensorInput ) {
// process the tensor
network.process(tensorInput, tensorOutput);
// now find the best score and sort them
categoryScores.reset();
double scoreBest = -Double.MAX_VALUE;
categoryBest = -1;
for (int category = 0; category < tensorOutput.length(1); category++) {
double score = tensorOutput.get(0, category);
categoryScores.grow().set(score, category);
if (score > scoreBest) {
scoreBest = score;
categoryBest = category;
}
}
// order the categories by most to least likely
Collections.sort(categoryScores.toList(), comparator);
}
@Override
public int getBestResult() {
return categoryBest;
}
@Override
public List<Score> getAllResults() {
return categoryScores.toList();
}
@Override
public List<String> getCategories() {
return categories;
}
public Planar<GrayF32> getImageRgb() {
return imageRgb;
}
}
|
darkma773r/commons-numbers | commons-numbers-gamma/src/test/java/org/apache/commons/numbers/gamma/LogBetaTest.java | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.commons.numbers.gamma;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
/**
* Tests for {@link LogBeta}.
*/
class LogBetaTest {
private static final double[][] LOG_BETA_REF = {
{0.125, 0.125, 2.750814190409515},
{0.125, 0.25, 2.444366899981226},
{0.125, 0.5, 2.230953804989556},
{0.125, 1.0, 2.079441541679836},
{0.125, 2.0, 1.961658506023452},
{0.125, 3.0, 1.901033884207018},
{0.125, 4.0, 1.860211889686763},
{0.125, 5.0, 1.829440231020009},
{0.125, 6.0, 1.804747618429637},
{0.125, 7.0, 1.784128331226902},
{0.125, 8.0, 1.766428754127501},
{0.125, 9.0, 1.750924567591535},
{0.125, 10.0, 1.7371312454592},
{0.125, 1000.0, 1.156003642015969},
{0.125, 1001.0, 1.155878649827818},
{0.125, 10000.0, .8681312798751318},
{0.25, 0.125, 2.444366899981226},
{0.25, 0.25, 2.003680106471455},
{0.25, 0.5, 1.657106516191482},
{0.25, 1.0, 1.386294361119891},
{0.25, 2.0, 1.163150809805681},
{0.25, 3.0, 1.045367774149297},
{0.25, 4.0, 0.965325066475761},
{0.25, 5.0, .9047004446593261},
{0.25, 6.0, .8559102804898941},
{0.25, 7.0, 0.815088285969639},
{0.25, 8.0, .7799969661583689},
{0.25, 9.0, .7492253074916152},
{0.25, 10.0, .7218263333035008},
{0.25, 1000.0, -.4388225372378877},
{0.25, 1001.0, -.4390725059930951},
{0.25, 10000.0, -1.014553193217846},
{0.5, 0.125, 2.230953804989556},
{0.5, 0.25, 1.657106516191482},
{0.5, 0.5, 1.1447298858494},
{0.5, 1.0, .6931471805599453},
{0.5, 2.0, .2876820724517809},
{0.5, 3.0, .06453852113757118},
// {0.5, 4.0, -.08961215868968714},
{0.5, 5.0, -.2073951943460706},
{0.5, 6.0, -.3027053741503954},
{0.5, 7.0, -.3827480818239319},
{0.5, 8.0, -.4517409533108833},
{0.5, 9.0, -.5123655751273182},
{0.5, 10.0, -.5664327963975939},
{0.5, 1000.0, -2.881387696571577},
{0.5, 1001.0, -2.881887571613228},
{0.5, 10000.0, -4.032792743063396},
{1.0, 0.125, 2.079441541679836},
{1.0, 0.25, 1.386294361119891},
{1.0, 0.5, .6931471805599453},
{1.0, 1.0, 0.0},
{1.0, 2.0, -.6931471805599453},
{1.0, 3.0, -1.09861228866811},
{1.0, 4.0, -1.386294361119891},
{1.0, 5.0, -1.6094379124341},
{1.0, 6.0, -1.791759469228055},
{1.0, 7.0, -1.945910149055313},
{1.0, 8.0, -2.079441541679836},
{1.0, 9.0, -2.19722457733622},
{1.0, 10.0, -2.302585092994046},
{1.0, 1000.0, -6.907755278982137},
{1.0, 1001.0, -6.90875477931522},
{1.0, 10000.0, -9.210340371976184},
{2.0, 0.125, 1.961658506023452},
{2.0, 0.25, 1.163150809805681},
{2.0, 0.5, .2876820724517809},
{2.0, 1.0, -.6931471805599453},
{2.0, 2.0, -1.791759469228055},
{2.0, 3.0, -2.484906649788},
{2.0, 4.0, -2.995732273553991},
{2.0, 5.0, -3.401197381662155},
{2.0, 6.0, -3.737669618283368},
{2.0, 7.0, -4.02535169073515},
{2.0, 8.0, -4.276666119016055},
{2.0, 9.0, -4.499809670330265},
{2.0, 10.0, -4.700480365792417},
{2.0, 1000.0, -13.81651005829736},
{2.0, 1001.0, -13.81850806096003},
{2.0, 10000.0, -18.4207807389527},
{3.0, 0.125, 1.901033884207018},
{3.0, 0.25, 1.045367774149297},
{3.0, 0.5, .06453852113757118},
{3.0, 1.0, -1.09861228866811},
{3.0, 2.0, -2.484906649788},
{3.0, 3.0, -3.401197381662155},
{3.0, 4.0, -4.0943445622221},
{3.0, 5.0, -4.653960350157523},
{3.0, 6.0, -5.123963979403259},
{3.0, 7.0, -5.529429087511423},
{3.0, 8.0, -5.886104031450156},
{3.0, 9.0, -6.20455776256869},
{3.0, 10.0, -6.492239835020471},
{3.0, 1000.0, -20.03311615938222},
{3.0, 1001.0, -20.03611166836202},
{3.0, 10000.0, -26.9381739103716},
{4.0, 0.125, 1.860211889686763},
{4.0, 0.25, 0.965325066475761},
// {4.0, 0.5, -.08961215868968714},
{4.0, 1.0, -1.386294361119891},
{4.0, 2.0, -2.995732273553991},
{4.0, 3.0, -4.0943445622221},
{4.0, 4.0, -4.941642422609304},
{4.0, 5.0, -5.634789603169249},
{4.0, 6.0, -6.222576268071369},
{4.0, 7.0, -6.733401891837359},
{4.0, 8.0, -7.185387015580416},
{4.0, 9.0, -7.590852123688581},
{4.0, 10.0, -7.958576903813898},
{4.0, 1000.0, -25.84525465867605},
{4.0, 1001.0, -25.84924667994559},
{4.0, 10000.0, -35.05020194868867},
{5.0, 0.125, 1.829440231020009},
{5.0, 0.25, .9047004446593261},
{5.0, 0.5, -.2073951943460706},
{5.0, 1.0, -1.6094379124341},
{5.0, 2.0, -3.401197381662155},
{5.0, 3.0, -4.653960350157523},
{5.0, 4.0, -5.634789603169249},
{5.0, 5.0, -6.445719819385578},
{5.0, 6.0, -7.138866999945524},
{5.0, 7.0, -7.745002803515839},
{5.0, 8.0, -8.283999304248526},
{5.0, 9.0, -8.769507120030227},
{5.0, 10.0, -9.211339872309265},
{5.0, 1000.0, -31.37070759780783},
{5.0, 1001.0, -31.37569513931887},
{5.0, 10000.0, -42.87464787956629},
{6.0, 0.125, 1.804747618429637},
{6.0, 0.25, .8559102804898941},
{6.0, 0.5, -.3027053741503954},
{6.0, 1.0, -1.791759469228055},
{6.0, 2.0, -3.737669618283368},
{6.0, 3.0, -5.123963979403259},
{6.0, 4.0, -6.222576268071369},
{6.0, 5.0, -7.138866999945524},
{6.0, 6.0, -7.927324360309794},
{6.0, 7.0, -8.620471540869739},
{6.0, 8.0, -9.239510749275963},
{6.0, 9.0, -9.799126537211386},
{6.0, 10.0, -10.30995216097738},
{6.0, 1000.0, -36.67401250586691},
{6.0, 1001.0, -36.67999457754446},
{6.0, 10000.0, -50.47605021415003},
{7.0, 0.125, 1.784128331226902},
{7.0, 0.25, 0.815088285969639},
{7.0, 0.5, -.3827480818239319},
{7.0, 1.0, -1.945910149055313},
{7.0, 2.0, -4.02535169073515},
{7.0, 3.0, -5.529429087511423},
{7.0, 4.0, -6.733401891837359},
{7.0, 5.0, -7.745002803515839},
{7.0, 6.0, -8.620471540869739},
{7.0, 7.0, -9.39366142910322},
{7.0, 8.0, -10.08680860966317},
{7.0, 9.0, -10.71541726908554},
{7.0, 10.0, -11.2907814139891},
{7.0, 1000.0, -41.79599038729854},
{7.0, 1001.0, -41.80296600103496},
{7.0, 10000.0, -57.89523093697012},
{8.0, 0.125, 1.766428754127501},
{8.0, 0.25, .7799969661583689},
{8.0, 0.5, -.4517409533108833},
{8.0, 1.0, -2.079441541679836},
{8.0, 2.0, -4.276666119016055},
{8.0, 3.0, -5.886104031450156},
{8.0, 4.0, -7.185387015580416},
{8.0, 5.0, -8.283999304248526},
{8.0, 6.0, -9.239510749275963},
{8.0, 7.0, -10.08680860966317},
{8.0, 8.0, -10.84894866171006},
{8.0, 9.0, -11.54209584227001},
{8.0, 10.0, -12.17808460899001},
{8.0, 1000.0, -46.76481113096179},
{8.0, 1001.0, -46.77277930061096},
{8.0, 10000.0, -65.16036091500527},
{9.0, 0.125, 1.750924567591535},
{9.0, 0.25, .7492253074916152},
{9.0, 0.5, -.5123655751273182},
{9.0, 1.0, -2.19722457733622},
{9.0, 2.0, -4.499809670330265},
{9.0, 3.0, -6.20455776256869},
{9.0, 4.0, -7.590852123688581},
{9.0, 5.0, -8.769507120030227},
{9.0, 6.0, -9.799126537211386},
{9.0, 7.0, -10.71541726908554},
{9.0, 8.0, -11.54209584227001},
{9.0, 9.0, -12.29586764464639},
{9.0, 10.0, -12.98901482520633},
{9.0, 1000.0, -51.60109303791327},
{9.0, 1001.0, -51.61005277928474},
{9.0, 10000.0, -72.29205942547217},
{10.0, 0.125, 1.7371312454592},
{10.0, 0.25, .7218263333035008},
{10.0, 0.5, -.5664327963975939},
{10.0, 1.0, -2.302585092994046},
{10.0, 2.0, -4.700480365792417},
{10.0, 3.0, -6.492239835020471},
{10.0, 4.0, -7.958576903813898},
{10.0, 5.0, -9.211339872309265},
{10.0, 6.0, -10.30995216097738},
{10.0, 7.0, -11.2907814139891},
{10.0, 8.0, -12.17808460899001},
{10.0, 9.0, -12.98901482520633},
{10.0, 10.0, -13.73622922703655},
{10.0, 1000.0, -56.32058348093065},
{10.0, 1001.0, -56.33053381178382},
{10.0, 10000.0, -79.30607481535498},
{1000.0, 0.125, 1.156003642015969},
{1000.0, 0.25, -.4388225372378877},
{1000.0, 0.5, -2.881387696571577},
{1000.0, 1.0, -6.907755278982137},
{1000.0, 2.0, -13.81651005829736},
{1000.0, 3.0, -20.03311615938222},
{1000.0, 4.0, -25.84525465867605},
{1000.0, 5.0, -31.37070759780783},
{1000.0, 6.0, -36.67401250586691},
{1000.0, 7.0, -41.79599038729854},
{1000.0, 8.0, -46.76481113096179},
{1000.0, 9.0, -51.60109303791327},
{1000.0, 10.0, -56.32058348093065},
{1000.0, 1000.0, -1388.482601635902},
{1000.0, 1001.0, -1389.175748816462},
{1000.0, 10000.0, -3353.484270767097},
{1001.0, 0.125, 1.155878649827818},
{1001.0, 0.25, -.4390725059930951},
{1001.0, 0.5, -2.881887571613228},
{1001.0, 1.0, -6.90875477931522},
{1001.0, 2.0, -13.81850806096003},
{1001.0, 3.0, -20.03611166836202},
{1001.0, 4.0, -25.84924667994559},
{1001.0, 5.0, -31.37569513931887},
{1001.0, 6.0, -36.67999457754446},
{1001.0, 7.0, -41.80296600103496},
{1001.0, 8.0, -46.77277930061096},
{1001.0, 9.0, -51.61005277928474},
{1001.0, 10.0, -56.33053381178382},
{1001.0, 1000.0, -1389.175748816462},
{1001.0, 1001.0, -1389.869395872064},
{1001.0, 10000.0, -3355.882166039895},
{10000.0, 0.125, .8681312798751318},
{10000.0, 0.25, -1.014553193217846},
{10000.0, 0.5, -4.032792743063396},
{10000.0, 1.0, -9.210340371976184},
{10000.0, 2.0, -18.4207807389527},
{10000.0, 3.0, -26.9381739103716},
{10000.0, 4.0, -35.05020194868867},
{10000.0, 5.0, -42.87464787956629},
{10000.0, 6.0, -50.47605021415003},
{10000.0, 7.0, -57.89523093697012},
{10000.0, 8.0, -65.16036091500527},
{10000.0, 9.0, -72.29205942547217},
{10000.0, 10.0, -79.30607481535498},
{10000.0, 1000.0, -3353.484270767097},
{10000.0, 1001.0, -3355.882166039895},
{10000.0, 10000.0, -13866.28325676141},
};
private static final double[][] LOG_GAMMA_MINUS_LOG_GAMMA_SUM_REF = {
// { 0.0 , 8.0 , 0.0 },
// { 0.0 , 9.0 , 0.0 },
{0.0, 10.0, 0.0},
{0.0, 11.0, 0.0},
{0.0, 12.0, 0.0},
{0.0, 13.0, 0.0},
{0.0, 14.0, 0.0},
{0.0, 15.0, 0.0},
{0.0, 16.0, 0.0},
{0.0, 17.0, 0.0},
{0.0, 18.0, 0.0},
// {1.0, 8.0, -2.079441541679836},
// {1.0, 9.0, -2.19722457733622},
{1.0, 10.0, -2.302585092994046},
{1.0, 11.0, -2.397895272798371},
{1.0, 12.0, -2.484906649788},
{1.0, 13.0, -2.564949357461537},
{1.0, 14.0, -2.639057329615258},
{1.0, 15.0, -2.70805020110221},
{1.0, 16.0, -2.772588722239781},
{1.0, 17.0, -2.833213344056216},
{1.0, 18.0, -2.890371757896165},
// {2.0, 8.0, -4.276666119016055},
// {2.0, 9.0, -4.499809670330265},
{2.0, 10.0, -4.700480365792417},
{2.0, 11.0, -4.882801922586371},
{2.0, 12.0, -5.049856007249537},
{2.0, 13.0, -5.204006687076795},
{2.0, 14.0, -5.347107530717468},
{2.0, 15.0, -5.480638923341991},
{2.0, 16.0, -5.605802066295998},
{2.0, 17.0, -5.723585101952381},
{2.0, 18.0, -5.834810737062605},
// {3.0, 8.0, -6.579251212010101},
// {3.0, 9.0, -6.897704943128636},
{3.0, 10.0, -7.185387015580416},
{3.0, 11.0, -7.447751280047908},
{3.0, 12.0, -7.688913336864796},
{3.0, 13.0, -7.912056888179006},
{3.0, 14.0, -8.11969625295725},
{3.0, 15.0, -8.313852267398207},
{3.0, 16.0, -8.496173824192162},
{3.0, 17.0, -8.668024081118821},
{3.0, 18.0, -8.830543010616596},
// {4.0, 8.0, -8.977146484808472},
// {4.0, 9.0, -9.382611592916636},
{4.0, 10.0, -9.750336373041954},
{4.0, 11.0, -10.08680860966317},
{4.0, 12.0, -10.39696353796701},
{4.0, 13.0, -10.68464561041879},
{4.0, 14.0, -10.95290959701347},
{4.0, 15.0, -11.20422402529437},
{4.0, 16.0, -11.4406128033586},
{4.0, 17.0, -11.66375635467281},
{4.0, 18.0, -11.87506544834002},
// {5.0, 8.0, -11.46205313459647},
// {5.0, 9.0, -11.94756095037817},
{5.0, 10.0, -12.38939370265721},
{5.0, 11.0, -12.79485881076538},
{5.0, 12.0, -13.16955226020679},
{5.0, 13.0, -13.517858954475},
{5.0, 14.0, -13.84328135490963},
{5.0, 15.0, -14.14866300446081},
{5.0, 16.0, -14.43634507691259},
{5.0, 17.0, -14.70827879239624},
{5.0, 18.0, -14.96610790169833},
// {6.0, 8.0, -14.02700249205801},
// {6.0, 9.0, -14.58661827999343},
{6.0, 10.0, -15.09744390375942},
{6.0, 11.0, -15.56744753300516},
{6.0, 12.0, -16.002765604263},
{6.0, 13.0, -16.40823071237117},
{6.0, 14.0, -16.78772033407607},
{6.0, 15.0, -17.14439527801481},
{6.0, 16.0, -17.48086751463602},
{6.0, 17.0, -17.79932124575455},
{6.0, 18.0, -18.10160211762749},
// {7.0, 8.0, -16.66605982167327},
// {7.0, 9.0, -17.29466848109564},
{7.0, 10.0, -17.8700326259992},
{7.0, 11.0, -18.40066087706137},
{7.0, 12.0, -18.89313736215917},
{7.0, 13.0, -19.35266969153761},
{7.0, 14.0, -19.78345260763006},
{7.0, 15.0, -20.18891771573823},
{7.0, 16.0, -20.57190996799433},
{7.0, 17.0, -20.9348154616837},
{7.0, 18.0, -21.27965594797543},
// {8.0, 8.0, -19.37411002277548},
// {8.0, 9.0, -20.06725720333542},
{8.0, 10.0, -20.70324597005542},
{8.0, 11.0, -21.29103263495754},
{8.0, 12.0, -21.83757634132561},
{8.0, 13.0, -22.3484019650916},
{8.0, 14.0, -22.82797504535349},
{8.0, 15.0, -23.27996016909654},
{8.0, 16.0, -23.70740418392348},
{8.0, 17.0, -24.11286929203165},
{8.0, 18.0, -24.49853177284363},
// {9.0, 8.0, -22.14669874501526},
// {9.0, 9.0, -22.90047054739164},
{9.0, 10.0, -23.59361772795159},
{9.0, 11.0, -24.23547161412398},
{9.0, 12.0, -24.8333086148796},
{9.0, 13.0, -25.39292440281502},
{9.0, 14.0, -25.9190174987118},
{9.0, 15.0, -26.41545438502569},
{9.0, 16.0, -26.88545801427143},
{9.0, 17.0, -27.33174511689985},
{9.0, 18.0, -27.75662831086511},
// {10.0, 8.0, -24.97991208907148},
// {10.0, 9.0, -25.7908423052878},
{10.0, 10.0, -26.53805670711802},
{10.0, 11.0, -27.23120388767797},
{10.0, 12.0, -27.87783105260302},
{10.0, 13.0, -28.48396685617334},
{10.0, 14.0, -29.05451171464095},
{10.0, 15.0, -29.59350821537364},
{10.0, 16.0, -30.10433383913963},
{10.0, 17.0, -30.58984165492133},
{10.0, 18.0, -31.05246517686944},
};
private static final double[][] SUM_DELTA_MINUS_DELTA_SUM_REF = {
{10.0, 10.0, .01249480717472882},
{10.0, 11.0, .01193628470267385},
{10.0, 12.0, .01148578547212797},
{10.0, 13.0, .01111659739668398},
{10.0, 14.0, .01080991216314295},
{10.0, 15.0, .01055214134859758},
{10.0, 16.0, .01033324912491747},
{10.0, 17.0, .01014568069918883},
{10.0, 18.0, .009983653199146491},
{10.0, 19.0, .009842674320242729},
{10.0, 20.0, 0.0097192081956071},
{11.0, 10.0, .01193628470267385},
{11.0, 11.0, .01135973290745925},
{11.0, 12.0, .01089355537047828},
{11.0, 13.0, .01051064829297728},
{11.0, 14.0, 0.0101918899639826},
{11.0, 15.0, .009923438811859604},
{11.0, 16.0, .009695052724952705},
{11.0, 17.0, 0.00949900745283617},
{11.0, 18.0, .009329379874933402},
{11.0, 19.0, 0.00918156080743147},
{11.0, 20.0, 0.00905191635141762},
{12.0, 10.0, .01148578547212797},
{12.0, 11.0, .01089355537047828},
{12.0, 12.0, .01041365883144029},
{12.0, 13.0, .01001867865848564},
{12.0, 14.0, 0.00968923999191334},
{12.0, 15.0, .009411294976563555},
{12.0, 16.0, .009174432043268762},
{12.0, 17.0, .008970786693291802},
{12.0, 18.0, .008794318926790865},
{12.0, 19.0, .008640321527910711},
{12.0, 20.0, .008505077879954796},
{13.0, 10.0, .01111659739668398},
{13.0, 11.0, .01051064829297728},
{13.0, 12.0, .01001867865848564},
{13.0, 13.0, .009613018147953376},
{13.0, 14.0, .009274085618154277},
{13.0, 15.0, 0.0089876637564166},
{13.0, 16.0, .008743200745261382},
{13.0, 17.0, .008532715206686251},
{13.0, 18.0, .008350069108807093},
{13.0, 19.0, .008190472517984874},
{13.0, 20.0, .008050138630244345},
{14.0, 10.0, .01080991216314295},
{14.0, 11.0, 0.0101918899639826},
{14.0, 12.0, 0.00968923999191334},
{14.0, 13.0, .009274085618154277},
{14.0, 14.0, .008926676241967286},
{14.0, 15.0, .008632654302369184},
{14.0, 16.0, .008381351102615795},
{14.0, 17.0, .008164687232662443},
{14.0, 18.0, .007976441942841219},
{14.0, 19.0, .007811755112234388},
{14.0, 20.0, .007666780069317652},
{15.0, 10.0, .01055214134859758},
{15.0, 11.0, .009923438811859604},
{15.0, 12.0, .009411294976563555},
{15.0, 13.0, 0.0089876637564166},
{15.0, 14.0, .008632654302369184},
{15.0, 15.0, 0.00833179217417291},
{15.0, 16.0, .008074310643041299},
{15.0, 17.0, .007852047581145882},
{15.0, 18.0, .007658712051540045},
{15.0, 19.0, .007489384065757007},
{15.0, 20.0, .007340165635725612},
{16.0, 10.0, .01033324912491747},
{16.0, 11.0, .009695052724952705},
{16.0, 12.0, .009174432043268762},
{16.0, 13.0, .008743200745261382},
{16.0, 14.0, .008381351102615795},
{16.0, 15.0, .008074310643041299},
{16.0, 16.0, .007811229919967624},
{16.0, 17.0, .007583876618287594},
{16.0, 18.0, .007385899933505551},
{16.0, 19.0, .007212328560607852},
{16.0, 20.0, .007059220321091879},
{17.0, 10.0, .01014568069918883},
{17.0, 11.0, 0.00949900745283617},
{17.0, 12.0, .008970786693291802},
{17.0, 13.0, .008532715206686251},
{17.0, 14.0, .008164687232662443},
{17.0, 15.0, .007852047581145882},
{17.0, 16.0, .007583876618287594},
{17.0, 17.0, .007351882161431358},
{17.0, 18.0, .007149662089534654},
{17.0, 19.0, .006972200907152378},
{17.0, 20.0, .006815518216094137},
{18.0, 10.0, .009983653199146491},
{18.0, 11.0, .009329379874933402},
{18.0, 12.0, .008794318926790865},
{18.0, 13.0, .008350069108807093},
{18.0, 14.0, .007976441942841219},
{18.0, 15.0, .007658712051540045},
{18.0, 16.0, .007385899933505551},
{18.0, 17.0, .007149662089534654},
{18.0, 18.0, .006943552208153373},
{18.0, 19.0, .006762516574228829},
{18.0, 20.0, .006602541598043117},
{19.0, 10.0, .009842674320242729},
{19.0, 11.0, 0.00918156080743147},
{19.0, 12.0, .008640321527910711},
{19.0, 13.0, .008190472517984874},
{19.0, 14.0, .007811755112234388},
{19.0, 15.0, .007489384065757007},
{19.0, 16.0, .007212328560607852},
{19.0, 17.0, .006972200907152378},
{19.0, 18.0, .006762516574228829},
{19.0, 19.0, .006578188655176814},
{19.0, 20.0, .006415174623476747},
{20.0, 10.0, 0.0097192081956071},
{20.0, 11.0, 0.00905191635141762},
{20.0, 12.0, .008505077879954796},
{20.0, 13.0, .008050138630244345},
{20.0, 14.0, .007666780069317652},
{20.0, 15.0, .007340165635725612},
{20.0, 16.0, .007059220321091879},
{20.0, 17.0, .006815518216094137},
{20.0, 18.0, .006602541598043117},
{20.0, 19.0, .006415174623476747},
{20.0, 20.0, .006249349445691423},
};
@Test
void testLogBeta() {
final int ulps = 3;
for (int i = 0; i < LOG_BETA_REF.length; i++) {
final double[] ref = LOG_BETA_REF[i];
final double a = ref[0];
final double b = ref[1];
final double expected = ref[2];
final double actual = LogBeta.value(a, b);
final double tol = ulps * Math.ulp(expected);
final StringBuilder builder = new StringBuilder();
builder.append(a).append(", ").append(b);
Assertions.assertEquals(expected, actual, tol, builder.toString());
}
}
@Test
void testLogBetaNanPositive() {
testLogBeta(Double.NaN, Double.NaN, 2);
}
@Test
void testLogBetaPositiveNan() {
testLogBeta(Double.NaN, 1, Double.NaN);
}
@Test
void testLogBetaNegativePositive() {
testLogBeta(Double.NaN, -1, 2);
}
@Test
void testLogBetaPositiveNegative() {
testLogBeta(Double.NaN, 1, -2);
}
@Test
void testLogBetaZeroPositive() {
testLogBeta(Double.NaN, 0, 2);
}
@Test
void testLogBetaPositiveZero() {
testLogBeta(Double.NaN, 1, 0);
}
@Test
void testLogBetaPositivePositive() {
testLogBeta(-0.693147180559945, 1, 2);
}
private void testLogBeta(double expected,
double a,
double b) {
double actual = LogBeta.value(a, b);
Assertions.assertEquals(expected, actual, 1e-15);
}
private static double logGammaMinusLogGammaSum(final double a,
final double b) {
/*
* Use reflection to access private method.
*/
try {
final Method m = LogBeta.class.getDeclaredMethod("logGammaMinusLogGammaSum",
Double.TYPE, Double.TYPE);
m.setAccessible(true);
return ((Double) m.invoke(null, a, b)).doubleValue();
} catch (NoSuchMethodException e) {
Assertions.fail(e.getMessage());
} catch (IllegalAccessException e) {
Assertions.fail(e.getMessage());
} catch (InvocationTargetException e) {
if (e.getTargetException() instanceof GammaException) {
throw (GammaException) e.getTargetException();
} else {
Assertions.fail(e.getTargetException().getMessage());
}
}
return Double.NaN;
}
@Test
void testLogGammaMinusLogGammaSum() {
final int ulps = 4;
for (int i = 0; i < LOG_GAMMA_MINUS_LOG_GAMMA_SUM_REF.length; i++) {
final double[] ref = LOG_GAMMA_MINUS_LOG_GAMMA_SUM_REF[i];
final double a = ref[0];
final double b = ref[1];
final double expected = ref[2];
final double actual = logGammaMinusLogGammaSum(a, b);
final double tol = ulps * Math.ulp(expected);
final StringBuilder builder = new StringBuilder();
builder.append(a).append(", ").append(b);
Assertions.assertEquals(expected, actual, tol, builder.toString());
}
}
@Test
void testLogGammaMinusLogGammaSumPrecondition1() {
Assertions.assertThrows(IllegalArgumentException.class,
() -> logGammaMinusLogGammaSum(-1, 8)
);
}
@Test
void testLogGammaMinusLogGammaSumPrecondition2() {
Assertions.assertThrows(IllegalArgumentException.class,
() -> logGammaMinusLogGammaSum(1, 7)
);
}
private static double sumDeltaMinusDeltaSum(final double a,
final double b) {
/*
* Use reflection to access private method.
*/
try {
final Method m = LogBeta.class.getDeclaredMethod("sumDeltaMinusDeltaSum",
Double.TYPE, Double.TYPE);
m.setAccessible(true);
return ((Double) m.invoke(null, a, b)).doubleValue();
} catch (NoSuchMethodException e) {
Assertions.fail(e.getMessage());
} catch (final IllegalAccessException e) {
Assertions.fail(e.getMessage());
} catch (final InvocationTargetException e) {
if (e.getTargetException() instanceof GammaException) {
throw (GammaException) e.getTargetException();
}
Assertions.fail(e.getTargetException().getMessage());
}
return Double.NaN;
}
@Test
void testSumDeltaMinusDeltaSum() {
final int ulps = 3;
for (int i = 0; i < SUM_DELTA_MINUS_DELTA_SUM_REF.length; i++) {
final double[] ref = SUM_DELTA_MINUS_DELTA_SUM_REF[i];
final double a = ref[0];
final double b = ref[1];
final double expected = ref[2];
final double actual = sumDeltaMinusDeltaSum(a, b);
final double tol = ulps * Math.ulp(expected);
final StringBuilder builder = new StringBuilder();
builder.append(a).append(", ").append(b);
Assertions.assertEquals(expected, actual, tol, builder.toString());
}
}
@Test
void testSumDeltaMinusDeltaSumPrecondition1() {
Assertions.assertThrows(IllegalArgumentException.class,
() -> sumDeltaMinusDeltaSum(9, 10)
);
}
@Test
void testSumDeltaMinusDeltaSumPrecondition2() {
Assertions.assertThrows(IllegalArgumentException.class,
() -> sumDeltaMinusDeltaSum(10, 9)
);
}
}
|
pmarkiewka/scm-manager | scm-core/src/main/java/sonia/scm/net/HttpConnectionOptions.java | /*
* MIT License
*
* Copyright (c) 2020-present Cloudogu GmbH and Contributors
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
package sonia.scm.net;
import com.google.common.annotations.VisibleForTesting;
import lombok.EqualsAndHashCode;
import lombok.Getter;
import lombok.ToString;
import javax.annotation.Nullable;
import javax.net.ssl.KeyManager;
import java.net.URL;
import java.util.Arrays;
import java.util.Optional;
import java.util.concurrent.TimeUnit;
/**
* Options for establishing a http connection.
* The options can be used to create a new http connection
* with {@link HttpURLConnectionFactory#create(URL, HttpConnectionOptions)}.
*
* @since 2.23.0
*/
@Getter
@ToString
@EqualsAndHashCode
public final class HttpConnectionOptions {
@VisibleForTesting
static final int DEFAULT_CONNECTION_TIMEOUT = 30000;
@VisibleForTesting
static final int DEFAULT_READ_TIMEOUT = 1200000;
@Nullable
private ProxyConfiguration proxyConfiguration;
@Nullable
private KeyManager[] keyManagers;
private boolean disableCertificateValidation = false;
private boolean disableHostnameValidation = false;
private int connectionTimeout = DEFAULT_CONNECTION_TIMEOUT;
private int readTimeout = DEFAULT_READ_TIMEOUT;
private boolean ignoreProxySettings = false;
/**
* Returns optional local proxy configuration.
* @return local proxy configuration or empty optional
*/
public Optional<ProxyConfiguration> getProxyConfiguration() {
return Optional.ofNullable(proxyConfiguration);
}
/**
* Return optional array of key managers for client certificate authentication.
*
* @return array of key managers or empty optional
*/
public Optional<KeyManager[]> getKeyManagers() {
if (keyManagers != null) {
return Optional.of(Arrays.copyOf(keyManagers, keyManagers.length));
}
return Optional.empty();
}
/**
* Disable certificate validation.
* <b>WARNING:</b> This option should only be used for internal test.
* It should never be used in production, because it is high security risk.
*
* @return {@code this}
*/
public HttpConnectionOptions withDisableCertificateValidation() {
this.disableCertificateValidation = true;
return this;
}
/**
* Disable hostname validation.
* <b>WARNING:</b> This option should only be used for internal test.
* It should never be used in production, because it is high security risk.
*
* @return {@code this}
*/
public HttpConnectionOptions withDisabledHostnameValidation() {
this.disableHostnameValidation = true;
return this;
}
/**
* Configure the connection timeout.
* @param timeout timeout
* @param unit unit of the timeout
* @return {@code this}
*/
public HttpConnectionOptions withConnectionTimeout(long timeout, TimeUnit unit) {
this.connectionTimeout = (int) unit.toMillis(timeout);
return this;
}
/**
* Configure the read timeout.
* @param timeout timeout
* @param unit unit of the timeout
* @return {@code this}
*/
public HttpConnectionOptions withReadTimeout(long timeout, TimeUnit unit) {
this.readTimeout = (int) unit.toMillis(timeout);
return this;
}
/**
* Configure a local proxy configuration, if no configuration is set the global default configuration will be used.
* @param proxyConfiguration local proxy configuration
* @return {@code this}
*/
public HttpConnectionOptions withProxyConfiguration(ProxyConfiguration proxyConfiguration) {
this.proxyConfiguration = proxyConfiguration;
return this;
}
/**
* Configure key managers for client certificate authentication.
* @param keyManagers key managers
* @return {@code this}
*/
public HttpConnectionOptions withKeyManagers(@Nullable KeyManager... keyManagers) {
if (keyManagers != null) {
this.keyManagers = Arrays.copyOf(keyManagers, keyManagers.length);
}
return this;
}
/**
* Ignore proxy settings completely regardless if a local proxy configuration or a global configuration is configured.
* @return {@code this}
*/
public HttpConnectionOptions withIgnoreProxySettings() {
this.ignoreProxySettings = true;
return this;
}
}
|
jforge/vaadin | test/dependency-rewrite-addon/src/main/java/com/vaadin/test/dependencyrewriteaddon/RewriteJQueryFilter.java | package com.vaadin.test.dependencyrewriteaddon;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import com.vaadin.server.DependencyFilter;
import com.vaadin.server.ServiceInitEvent;
import com.vaadin.server.VaadinServiceInitListener;
import com.vaadin.ui.Dependency;
import com.vaadin.ui.Dependency.Type;
public class RewriteJQueryFilter
implements DependencyFilter, VaadinServiceInitListener {
@Override
public List<Dependency> filter(List<Dependency> dependencies,
FilterContext filterContext) {
List<Dependency> filtered = new ArrayList<>();
for (Dependency dependency : dependencies) {
if (dependency.getType() == Type.JAVASCRIPT && dependency.getUrl()
.toLowerCase(Locale.ROOT).contains("jquery")) {
filtered.add(
new Dependency(Type.JAVASCRIPT, "vaadin://jquery.js"));
} else {
filtered.add(dependency);
}
}
return filtered;
}
// for compactness, implementing the init listener here
@Override
public void serviceInit(ServiceInitEvent event) {
event.addDependencyFilter(this);
}
}
|
AlexRogalskiy/DevArtifacts | master/Currency-Converter-master/Currency-Converter-master/js/translation.js | <filename>master/Currency-Converter-master/Currency-Converter-master/js/translation.js
var Translation = {
'it': {
'app-description': 'Currency Converter è una semplice applicazione che ti aiuta a convertire da una valuta ad un\'altra. È anche possibile aggiornare i tassi di cambio ogni volta che si desidera così da avere sempre dei tassi di conversione aggiornati.',
'convert-title': 'Converti',
'from-value-label': 'Valore:',
'from-type-label': 'Da Valuta:',
'to-type-label': 'A Valuta:',
'result-title': 'Risultato',
'copyright-title': 'Creata da Aurelio De Rosa',
'credits-button': 'Crediti',
'update-button': 'Aggiorna dati',
'submit-button': 'Converti',
'reset-button': 'Azzera dati',
'last-update-label': 'Ultimo aggiornamento cambi:'
},
'fr': {
'app-description': 'Currency Converter est simple une application qui vous permet de convertir à partir d\'un monnaie à une autre. Vous pouvez également mettre à jour les taux de change chaque fois que vous le voulez et vous aurez toujours actualisés les résultats en utilisant les taux du marché moyen en direct',
'convert-title': 'Effectuer la convertion',
'from-value-label': 'Valeur:',
'from-type-label': 'À partir de cette devise:',
'to-type-label': 'Vers cette devise:',
'result-title': 'Résultat',
'copyright-title': 'Crée par <NAME>',
'credits-button': 'Crédits',
'update-button': 'Mettre à jour les données',
'submit-button': 'Convertir',
'reset-button': 'Réinitialiser les données',
'last-update-label': 'Dernière mise à jour des changements:'
},
'es': {
'app-description': 'Currency Converter es una sencilla aplicación que te ayuda a convertir de un moneda en otra. También puede actualizar los tipos de cambio y tener las tasas de conversión actualizadas.',
'convert-title': 'Convertir',
'from-value-label': 'Valor:',
'from-type-label': 'De:',
'to-type-label': 'A:',
'result-title': 'Resultado',
'copyright-title': 'Creada por <NAME>',
'credits-button': 'Créditos',
'update-button': 'Actualizar los datos',
'submit-button': 'Convertir',
'reset-button': 'Restablecer los datos',
'last-update-label': 'Cambios de última actualización:'
}
} |
swingflip/C64_mini_VICE | src/arch/msdos/cbmcharsets.c | /*
* cbmcharsets.c - CBM lookalike character sets.
*
* Written by
* <NAME> / STA <<EMAIL>>
*
* This file is part of VICE, the Versatile Commodore Emulator.
* See README for copyright notice.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA.
*
*/
#include "types.h"
#include "cbmcharsets.h"
BYTE cbm_charset_1[] = {
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x7e, 0x7e, 0x81, 0x81, 0xa5, 0xa5, 0x81, 0x81,
0x99, 0x99, 0x81, 0x81, 0x7e, 0x7e, 0x00, 0x00,
0x7e, 0x7e, 0xff, 0xff, 0xdb, 0xdb, 0xff, 0xff,
0xe7, 0xe7, 0xff, 0xff, 0x7e, 0x7e, 0x00, 0x00,
0x36, 0x36, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f,
0x3e, 0x3e, 0x1c, 0x1c, 0x08, 0x08, 0x00, 0x00,
0x08, 0x08, 0x1c, 0x1c, 0x3e, 0x3e, 0x7f, 0x7f,
0x3e, 0x3e, 0x1c, 0x1c, 0x08, 0x08, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x66, 0x66, 0x66, 0x66,
0x18, 0x18, 0x18, 0x18, 0x3c, 0x3c, 0x00, 0x00,
0x08, 0x08, 0x1c, 0x1c, 0x3e, 0x3e, 0x7f, 0x7f,
0x7f, 0x7f, 0x1c, 0x1c, 0x3e, 0x3e, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x18, 0x18, 0x3c, 0x3c,
0x3c, 0x3c, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0xe7, 0xe7, 0xc3, 0xc3,
0xc3, 0xc3, 0xe7, 0xe7, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x18, 0x18, 0x24, 0x24,
0x24, 0x24, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0xe7, 0xe7, 0xdb, 0xdb,
0xdb, 0xdb, 0xe7, 0xe7, 0xff, 0xff, 0xff, 0xff,
0x0e, 0x0e, 0x05, 0x05, 0x08, 0x08, 0x38, 0x38,
0x44, 0x44, 0x44, 0x44, 0x38, 0x38, 0x00, 0x00,
0x00, 0x00, 0x38, 0x38, 0x44, 0x44, 0x44, 0x44,
0x38, 0x38, 0x10, 0x10, 0x38, 0x38, 0x10, 0x10,
0x08, 0x08, 0x0c, 0x0c, 0x08, 0x08, 0x08, 0x08,
0x08, 0x08, 0x38, 0x38, 0x38, 0x38, 0x00, 0x00,
0x3e, 0x3e, 0x22, 0x22, 0x3e, 0x3e, 0x22, 0x22,
0x22, 0x22, 0x26, 0x26, 0x66, 0x66, 0x60, 0x60,
0x08, 0x08, 0x2a, 0x2a, 0x14, 0x14, 0x63, 0x63,
0x14, 0x14, 0x2a, 0x2a, 0x08, 0x08, 0x00, 0x00,
0x00, 0x00, 0x60, 0x60, 0x78, 0x78, 0x7e, 0x7e,
0x7e, 0x7e, 0x78, 0x78, 0x60, 0x60, 0x00, 0x00,
0x00, 0x00, 0x06, 0x06, 0x1e, 0x1e, 0x7e, 0x7e,
0x7e, 0x7e, 0x1e, 0x1e, 0x06, 0x06, 0x00, 0x00,
0x18, 0x18, 0x3c, 0x3c, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x3c, 0x3c, 0x18, 0x18, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x00, 0x00, 0x66, 0x66, 0x00, 0x00,
0x00, 0x00, 0x3f, 0x3f, 0x5b, 0x5b, 0x1b, 0x1b,
0x1b, 0x1b, 0x1b, 0x1b, 0x1b, 0x1b, 0x00, 0x00,
0x3c, 0x3c, 0x60, 0x60, 0x3c, 0x3c, 0x66, 0x66,
0x3c, 0x3c, 0x06, 0x06, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x3c, 0x3c,
0x3c, 0x3c, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x3c, 0x3c, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x3c, 0x3c, 0x18, 0x18, 0x7e, 0x7e,
0x00, 0x00, 0x18, 0x18, 0x3c, 0x3c, 0x7e, 0x7e,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x7e, 0x7e, 0x3c, 0x3c, 0x18, 0x18, 0x00, 0x00,
0x00, 0x00, 0x08, 0x08, 0x0c, 0x0c, 0xfe, 0xfe,
0xfe, 0xfe, 0x0c, 0x0c, 0x08, 0x08, 0x00, 0x00,
0x00, 0x00, 0x10, 0x10, 0x30, 0x30, 0x7f, 0x7f,
0x7f, 0x7f, 0x30, 0x30, 0x10, 0x10, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x60, 0x60, 0x60, 0x60,
0x7e, 0x7e, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
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0x0c, 0x0c, 0x18, 0x18, 0x30, 0x30, 0x00, 0x00,
0x00, 0x00, 0x66, 0x66, 0x3c, 0x3c, 0xff, 0xff,
0x3c, 0x3c, 0x66, 0x66, 0x00, 0x00, 0x00, 0x00,
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0x3c, 0x3c, 0x66, 0x66, 0x6e, 0x6e, 0x76, 0x76,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x38, 0x38, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x7e, 0x7e, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x06, 0x06, 0x0c, 0x0c,
0x30, 0x30, 0x60, 0x60, 0x7e, 0x7e, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x06, 0x06, 0x1c, 0x1c,
0x06, 0x06, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x06, 0x06, 0x0e, 0x0e, 0x1e, 0x1e, 0x66, 0x66,
0x7f, 0x7f, 0x06, 0x06, 0x06, 0x06, 0x00, 0x00,
0x7e, 0x7e, 0x60, 0x60, 0x7c, 0x7c, 0x06, 0x06,
0x06, 0x06, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x60, 0x60, 0x7c, 0x7c,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x7e, 0x7e, 0x66, 0x66, 0x0c, 0x0c, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x66, 0x66, 0x3e, 0x3e,
0x06, 0x06, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
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0x0e, 0x0e, 0x18, 0x18, 0x30, 0x30, 0x60, 0x60,
0x30, 0x30, 0x18, 0x18, 0x0e, 0x0e, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x7e, 0x7e, 0x00, 0x00,
0x7e, 0x7e, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x70, 0x70, 0x18, 0x18, 0x0c, 0x0c, 0x06, 0x06,
0x0c, 0x0c, 0x18, 0x18, 0x70, 0x70, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x06, 0x06, 0x0c, 0x0c,
0x18, 0x18, 0x00, 0x00, 0x18, 0x18, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x6e, 0x6e, 0x6e, 0x6e,
0x60, 0x60, 0x62, 0x62, 0x3c, 0x3c, 0x00, 0x00,
0x18, 0x18, 0x3c, 0x3c, 0x66, 0x66, 0x7e, 0x7e,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x00, 0x00,
0x7c, 0x7c, 0x66, 0x66, 0x66, 0x66, 0x7c, 0x7c,
0x66, 0x66, 0x66, 0x66, 0x7c, 0x7c, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x60, 0x60, 0x60, 0x60,
0x60, 0x60, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x78, 0x78, 0x6c, 0x6c, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x6c, 0x6c, 0x78, 0x78, 0x00, 0x00,
0x7e, 0x7e, 0x60, 0x60, 0x60, 0x60, 0x78, 0x78,
0x60, 0x60, 0x60, 0x60, 0x7e, 0x7e, 0x00, 0x00,
0x7e, 0x7e, 0x60, 0x60, 0x60, 0x60, 0x78, 0x78,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x60, 0x60, 0x6e, 0x6e,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x7e, 0x7e,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x00, 0x00,
0x3c, 0x3c, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x3c, 0x3c, 0x00, 0x00,
0x1e, 0x1e, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c,
0x0c, 0x0c, 0x6c, 0x6c, 0x38, 0x38, 0x00, 0x00,
0x66, 0x66, 0x6c, 0x6c, 0x78, 0x78, 0x70, 0x70,
0x78, 0x78, 0x6c, 0x6c, 0x66, 0x66, 0x00, 0x00,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60,
0x60, 0x60, 0x60, 0x60, 0x7e, 0x7e, 0x00, 0x00,
0x63, 0x63, 0x77, 0x77, 0x7f, 0x7f, 0x6b, 0x6b,
0x63, 0x63, 0x63, 0x63, 0x63, 0x63, 0x00, 0x00,
0x66, 0x66, 0x76, 0x76, 0x7e, 0x7e, 0x7e, 0x7e,
0x6e, 0x6e, 0x66, 0x66, 0x66, 0x66, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x7c, 0x7c, 0x66, 0x66, 0x66, 0x66, 0x7c, 0x7c,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x3c, 0x3c, 0x0e, 0x0e, 0x00, 0x00,
0x7c, 0x7c, 0x66, 0x66, 0x66, 0x66, 0x7c, 0x7c,
0x78, 0x78, 0x6c, 0x6c, 0x66, 0x66, 0x00, 0x00,
0x3c, 0x3c, 0x66, 0x66, 0x60, 0x60, 0x3c, 0x3c,
0x06, 0x06, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x7e, 0x7e, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x3c, 0x3c, 0x18, 0x18, 0x00, 0x00,
0x63, 0x63, 0x63, 0x63, 0x63, 0x63, 0x6b, 0x6b,
0x7f, 0x7f, 0x77, 0x77, 0x63, 0x63, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x18, 0x18,
0x3c, 0x3c, 0x66, 0x66, 0x66, 0x66, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x00, 0x00,
0x7e, 0x7e, 0x06, 0x06, 0x0c, 0x0c, 0x18, 0x18,
0x30, 0x30, 0x60, 0x60, 0x7e, 0x7e, 0x00, 0x00,
0x3c, 0x3c, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30,
0x30, 0x30, 0x30, 0x30, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x60, 0x60, 0x30, 0x30, 0x18, 0x18,
0x0c, 0x0c, 0x06, 0x06, 0x03, 0x03, 0x00, 0x00,
0x3c, 0x3c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c,
0x0c, 0x0c, 0x0c, 0x0c, 0x3c, 0x3c, 0x00, 0x00,
0x18, 0x18, 0x3c, 0x3c, 0x66, 0x66, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0x00, 0x00,
0x30, 0x30, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x3c, 0x3c, 0x06, 0x06,
0x3e, 0x3e, 0x66, 0x66, 0x3e, 0x3e, 0x00, 0x00,
0x00, 0x00, 0x60, 0x60, 0x60, 0x60, 0x7c, 0x7c,
0x66, 0x66, 0x66, 0x66, 0x7c, 0x7c, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x3c, 0x3c, 0x60, 0x60,
0x60, 0x60, 0x60, 0x60, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x06, 0x06, 0x06, 0x06, 0x3e, 0x3e,
0x66, 0x66, 0x66, 0x66, 0x3e, 0x3e, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x3c, 0x3c, 0x66, 0x66,
0x7e, 0x7e, 0x60, 0x60, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x0e, 0x0e, 0x18, 0x18, 0x3e, 0x3e,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x3e, 0x3e, 0x66, 0x66,
0x66, 0x66, 0x3e, 0x3e, 0x06, 0x06, 0x7c, 0x7c,
0x00, 0x00, 0x60, 0x60, 0x60, 0x60, 0x7c, 0x7c,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x00, 0x00,
0x00, 0x00, 0x18, 0x18, 0x00, 0x00, 0x38, 0x38,
0x18, 0x18, 0x18, 0x18, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x06, 0x06, 0x00, 0x00, 0x06, 0x06,
0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x3c, 0x3c,
0x00, 0x00, 0x60, 0x60, 0x60, 0x60, 0x6c, 0x6c,
0x78, 0x78, 0x6c, 0x6c, 0x66, 0x66, 0x00, 0x00,
0x00, 0x00, 0x38, 0x38, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x7f, 0x7f,
0x7f, 0x7f, 0x6b, 0x6b, 0x63, 0x63, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x7c, 0x7c, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x3c, 0x3c, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x7c, 0x7c, 0x66, 0x66,
0x66, 0x66, 0x7c, 0x7c, 0x60, 0x60, 0x60, 0x60,
0x00, 0x00, 0x00, 0x00, 0x3e, 0x3e, 0x66, 0x66,
0x66, 0x66, 0x3e, 0x3e, 0x06, 0x06, 0x06, 0x06,
0x00, 0x00, 0x00, 0x00, 0x7c, 0x7c, 0x66, 0x66,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x3e, 0x3e, 0x60, 0x60,
0x3c, 0x3c, 0x06, 0x06, 0x7c, 0x7c, 0x00, 0x00,
0x00, 0x00, 0x18, 0x18, 0x7e, 0x7e, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x0e, 0x0e, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x3e, 0x3e, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x3c, 0x3c, 0x18, 0x18, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x63, 0x63, 0x6b, 0x6b,
0x7f, 0x7f, 0x3e, 0x3e, 0x36, 0x36, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x3c, 0x3c,
0x18, 0x18, 0x3c, 0x3c, 0x66, 0x66, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x3e, 0x3e, 0x0c, 0x0c, 0x78, 0x78,
0x00, 0x00, 0x00, 0x00, 0x7e, 0x7e, 0x0c, 0x0c,
0x18, 0x18, 0x30, 0x30, 0x7e, 0x7e, 0x00, 0x00,
0x1c, 0x1c, 0x30, 0x30, 0x30, 0x30, 0x60, 0x60,
0x30, 0x30, 0x30, 0x30, 0x1c, 0x1c, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x00, 0x00,
0x00, 0x00, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x38, 0x38, 0x0c, 0x0c, 0x0c, 0x0c, 0x06, 0x06,
0x0c, 0x0c, 0x0c, 0x0c, 0x38, 0x38, 0x00, 0x00,
0x3b, 0x3b, 0x6e, 0x6e, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x18, 0x18, 0x3c, 0x3c,
0x66, 0x66, 0x66, 0x66, 0x7e, 0x7e, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x08, 0x08, 0x1c, 0x1c, 0x3e, 0x3e, 0x7f, 0x7f,
0x7f, 0x7f, 0x1c, 0x1c, 0x3e, 0x3e, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00,
0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30,
0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30,
0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c,
0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xe0, 0xe0,
0xf0, 0xf0, 0x38, 0x38, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x1c, 0x1c, 0x0f, 0x0f,
0x07, 0x07, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x38, 0x38, 0xf0, 0xf0,
0xe0, 0xe0, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xff, 0xff, 0xff, 0xff,
0xc0, 0xc0, 0xe0, 0xe0, 0x70, 0x70, 0x38, 0x38,
0x1c, 0x1c, 0x0e, 0x0e, 0x07, 0x07, 0x03, 0x03,
0x03, 0x03, 0x07, 0x07, 0x0e, 0x0e, 0x1c, 0x1c,
0x38, 0x38, 0x70, 0x70, 0xe0, 0xe0, 0xc0, 0xc0,
0xff, 0xff, 0xff, 0xff, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xff, 0xff, 0xff, 0xff, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x00, 0x00, 0x3c, 0x3c, 0x7e, 0x7e, 0x7e, 0x7e,
0x7e, 0x7e, 0x7e, 0x7e, 0x3c, 0x3c, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x36, 0x36, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f,
0x3e, 0x3e, 0x1c, 0x1c, 0x08, 0x08, 0x00, 0x00,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x07,
0x0f, 0x0f, 0x1c, 0x1c, 0x18, 0x18, 0x18, 0x18,
0xc3, 0xc3, 0xe7, 0xe7, 0x7e, 0x7e, 0x3c, 0x3c,
0x3c, 0x3c, 0x7e, 0x7e, 0xe7, 0xe7, 0xc3, 0xc3,
0x00, 0x00, 0x3c, 0x3c, 0x7e, 0x7e, 0x66, 0x66,
0x66, 0x66, 0x7e, 0x7e, 0x3c, 0x3c, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x66, 0x66, 0x66, 0x66,
0x18, 0x18, 0x18, 0x18, 0x3c, 0x3c, 0x00, 0x00,
0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06,
0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06,
0x08, 0x08, 0x1c, 0x1c, 0x3e, 0x3e, 0x7f, 0x7f,
0x3e, 0x3e, 0x1c, 0x1c, 0x08, 0x08, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff, 0xff,
0xff, 0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0xc0, 0xc0, 0xc0, 0xc0, 0x30, 0x30, 0x30, 0x30,
0xc0, 0xc0, 0xc0, 0xc0, 0x30, 0x30, 0x30, 0x30,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x03, 0x03, 0x3e, 0x3e,
0x76, 0x76, 0x36, 0x36, 0x36, 0x36, 0x00, 0x00,
0xff, 0xff, 0x7f, 0x7f, 0x3f, 0x3f, 0x1f, 0x1f,
0x0f, 0x0f, 0x07, 0x07, 0x03, 0x03, 0x01, 0x01,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8, 0xf8,
0xf8, 0xf8, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x18, 0x18, 0x00, 0x00, 0x18, 0x18, 0x30, 0x30,
0x60, 0x60, 0x66, 0x66, 0x3c, 0x3c, 0x00, 0x00,
0x0c, 0x0c, 0x12, 0x12, 0x30, 0x30, 0x7c, 0x7c,
0x30, 0x30, 0x62, 0x62, 0xfc, 0xfc, 0x00, 0x00,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0x33, 0x33, 0x99, 0x99, 0xcc, 0xcc, 0x66, 0x66,
0x33, 0x33, 0x99, 0x99, 0xcc, 0xcc, 0x66, 0x66,
0xcc, 0xcc, 0x99, 0x99, 0x33, 0x33, 0x66, 0x66,
0xcc, 0xcc, 0x99, 0x99, 0x33, 0x33, 0x66, 0x66,
0x18, 0x18, 0x00, 0x00, 0x00, 0x00, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x00, 0x00,
0x00, 0x00, 0x22, 0x22, 0x66, 0x66, 0xcc, 0xcc,
0xcc, 0xcc, 0x66, 0x66, 0x22, 0x22, 0x00, 0x00,
0x00, 0x00, 0x88, 0x88, 0xcc, 0xcc, 0x66, 0x66,
0x66, 0x66, 0xcc, 0xcc, 0x88, 0x88, 0x00, 0x00,
0x11, 0x11, 0x44, 0x44, 0x11, 0x11, 0x44, 0x44,
0x11, 0x11, 0x44, 0x44, 0x11, 0x11, 0x44, 0x44,
0x55, 0x55, 0xaa, 0xaa, 0x55, 0x55, 0xaa, 0xaa,
0x55, 0x55, 0xaa, 0xaa, 0x55, 0x55, 0xaa, 0xaa,
0xee, 0xee, 0xbb, 0xbb, 0xee, 0xee, 0xbb, 0xbb,
0xee, 0xee, 0xbb, 0xbb, 0xee, 0xee, 0xbb, 0xbb,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8, 0xf8,
0xf8, 0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0xf8, 0xf8, 0xf8, 0xf8, 0x18, 0x18,
0x18, 0x18, 0xf8, 0xf8, 0xf8, 0xf8, 0x18, 0x18,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xe6, 0xe6,
0xe6, 0xe6, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xfe, 0xfe,
0xfe, 0xfe, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0xf8, 0xf8, 0xf8, 0xf8, 0x18, 0x18,
0x18, 0x18, 0xf8, 0xf8, 0xf8, 0xf8, 0x18, 0x18,
0x66, 0x66, 0xe6, 0xe6, 0xe6, 0xe6, 0x06, 0x06,
0x06, 0x06, 0xe6, 0xe6, 0xe6, 0xe6, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0xfe, 0xfe, 0xfe, 0xfe, 0x06, 0x06,
0x06, 0x06, 0xe6, 0xe6, 0xe6, 0xe6, 0x66, 0x66,
0x66, 0x66, 0xe6, 0xe6, 0xe6, 0xe6, 0x06, 0x06,
0x06, 0x06, 0xfe, 0xfe, 0xfe, 0xfe, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xfe, 0xfe,
0xfe, 0xfe, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0xf8, 0xf8, 0xf8, 0xf8, 0x18, 0x18,
0x18, 0x18, 0xf8, 0xf8, 0xf8, 0xf8, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xf8, 0xf8,
0xf8, 0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f, 0x1f,
0x1f, 0x1f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xff, 0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f, 0x1f,
0x1f, 0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff, 0xff,
0xff, 0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x1f, 0x1f, 0x1f, 0x1f, 0x18, 0x18,
0x18, 0x18, 0x1f, 0x1f, 0x1f, 0x1f, 0x18, 0x18,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x67, 0x67,
0x67, 0x67, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x67, 0x67, 0x67, 0x67, 0x60, 0x60,
0x60, 0x60, 0x7f, 0x7f, 0x7f, 0x7f, 0x00, 0x00,
0x00, 0x00, 0x7f, 0x7f, 0x7f, 0x7f, 0x60, 0x60,
0x60, 0x60, 0x67, 0x67, 0x67, 0x67, 0x66, 0x66,
0x66, 0x66, 0xe7, 0xe7, 0xe7, 0xe7, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0xe7, 0xe7, 0xe7, 0xe7, 0x66, 0x66,
0x66, 0x66, 0x67, 0x67, 0x67, 0x67, 0x60, 0x60,
0x60, 0x60, 0x67, 0x67, 0x67, 0x67, 0x66, 0x66,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x66, 0x66, 0xe7, 0xe7, 0xe7, 0xe7, 0x00, 0x00,
0x00, 0x00, 0xe7, 0xe7, 0xe7, 0xe7, 0x66, 0x66,
0x18, 0x18, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xff, 0xff, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x7f, 0x7f,
0x7f, 0x7f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x1f, 0x1f, 0x1f, 0x1f, 0x18, 0x18,
0x18, 0x18, 0x1f, 0x1f, 0x1f, 0x1f, 0x00, 0x00,
0x00, 0x00, 0x1f, 0x1f, 0x1f, 0x1f, 0x18, 0x18,
0x18, 0x18, 0x1f, 0x1f, 0x1f, 0x1f, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x7f, 0x7f,
0x7f, 0x7f, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xff, 0xff,
0xff, 0xff, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x18, 0x18, 0xff, 0xff, 0xff, 0xff, 0x18, 0x18,
0x18, 0x18, 0xff, 0xff, 0xff, 0xff, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8, 0xf8,
0xf8, 0xf8, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x1f, 0x1f,
0x1f, 0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0xff, 0xff, 0xfe, 0xfe, 0xfc, 0xfc, 0xf8, 0xf8,
0xf0, 0xf0, 0xe0, 0xe0, 0xc0, 0xc0, 0x80, 0x80,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f, 0x1f,
0x1f, 0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f, 0x1f,
0x1f, 0x1f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xf8, 0xf8,
0xf8, 0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x1f, 0x1f,
0x1f, 0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xff, 0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8, 0xf8,
0xf8, 0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0,
0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0,
0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07,
0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07,
0xff, 0xff, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x18, 0x18,
0x18, 0x18, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x01, 0x01, 0x03, 0x03, 0x06, 0x06, 0x6c, 0x6c,
0x78, 0x78, 0x70, 0x70, 0x60, 0x60, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x7c, 0x7c, 0x7c, 0x7c,
0x7c, 0x7c, 0x7c, 0x7c, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00
};
BYTE cbm_charset_2[] = {
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x7e, 0x81, 0xa5, 0x81, 0x81, 0xbd,
0x99, 0x81, 0x81, 0x7e, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x7e, 0xff, 0xdb, 0xff, 0xff, 0xc3,
0xe7, 0xff, 0xff, 0x7e, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x36, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f,
0x3e, 0x1c, 0x1c, 0x08, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x18, 0x18, 0x3c, 0x7e, 0xff, 0xff,
0x7e, 0x3c, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
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0x00, 0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x3c,
0x18, 0x3c, 0x66, 0x66, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x66, 0x66, 0x66,
0x66, 0x66, 0x3e, 0x06, 0x0c, 0x78, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x7e, 0x06, 0x0c,
0x18, 0x30, 0x60, 0x7e, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x0e, 0x18, 0x18, 0x18, 0x70, 0x18,
0x18, 0x18, 0x18, 0x0e, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x18, 0x18, 0x18, 0x18, 0x00, 0x18,
0x18, 0x18, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x70, 0x18, 0x18, 0x18, 0x0e, 0x18,
0x18, 0x18, 0x18, 0x70, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x33, 0x7e, 0xcc, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x18, 0x3c, 0x66,
0x66, 0x7e, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff,
0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x18, 0x3c, 0x7e, 0xff, 0xff, 0xff,
0x7e, 0x18, 0x18, 0x3c, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff,
0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00,
0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30,
0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30, 0x30,
0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c,
0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c, 0x0c,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xe0,
0xf0, 0x38, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1c, 0x0f,
0x07, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x38, 0xf0,
0xe0, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xff, 0xff,
0x80, 0xc0, 0xc0, 0x60, 0x60, 0x30, 0x30, 0x18,
0x18, 0x0c, 0x0c, 0x06, 0x06, 0x03, 0x03, 0x01,
0x01, 0x03, 0x03, 0x06, 0x06, 0x0c, 0x0c, 0x18,
0x18, 0x30, 0x30, 0x60, 0x60, 0xc0, 0xc0, 0x80,
0xff, 0xff, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xff, 0xff, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x00, 0x00, 0x00, 0x00, 0x00, 0x3c, 0x7e, 0x7e,
0x7e, 0x7e, 0x3c, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0x00,
0x00, 0x00, 0x36, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f,
0x3e, 0x1c, 0x1c, 0x08, 0x00, 0x00, 0x00, 0x00,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60,
0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60, 0x60,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07,
0x0f, 0x1c, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x81, 0xc3, 0xc3, 0x66, 0x66, 0x3c, 0x3c, 0x18,
0x18, 0x3c, 0x3c, 0x66, 0x66, 0xc3, 0xc3, 0x81,
0x00, 0x00, 0x00, 0x00, 0x00, 0x3c, 0x7e, 0x66,
0x66, 0x7e, 0x3c, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x18, 0x18, 0x18, 0x66, 0x66, 0x66,
0x18, 0x18, 0x18, 0x3c, 0x00, 0x00, 0x00, 0x00,
0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06,
0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06, 0x06,
0x00, 0x00, 0x18, 0x18, 0x3c, 0x7e, 0xff, 0xff,
0x7e, 0x3c, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff,
0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0xc0, 0xc0, 0xc0, 0xc0, 0x30, 0x30, 0x30, 0x30,
0xc0, 0xc0, 0xc0, 0xc0, 0x30, 0x30, 0x30, 0x30,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x03, 0x3e, 0x76,
0x76, 0x36, 0x36, 0x36, 0x36, 0x00, 0x00, 0x00,
0xff, 0xff, 0x7f, 0x7f, 0x3f, 0x3f, 0x1f, 0x1f,
0x0f, 0x0f, 0x07, 0x07, 0x03, 0x03, 0x01, 0x01,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8,
0xf8, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x00, 0x00, 0x18, 0x18, 0x00, 0x18, 0x18, 0x18,
0x0c, 0x06, 0x66, 0x3c, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x0c, 0x12, 0x32, 0x30, 0x7c, 0x30,
0x30, 0x62, 0x62, 0xfc, 0x00, 0x00, 0x00, 0x00,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0x33, 0x33, 0x99, 0x99, 0xcc, 0xcc, 0x66, 0x66,
0x33, 0x33, 0x99, 0x99, 0xcc, 0xcc, 0x66, 0x66,
0xcc, 0xcc, 0x99, 0x99, 0x33, 0x33, 0x66, 0x66,
0xcc, 0xcc, 0x99, 0x99, 0x33, 0x33, 0x66, 0x66,
0x00, 0x00, 0x18, 0x18, 0x00, 0x00, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x22, 0x66, 0xcc,
0xcc, 0x66, 0x22, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x88, 0xcc, 0x66,
0x66, 0xcc, 0x88, 0x00, 0x00, 0x00, 0x00, 0x00,
0x11, 0x11, 0x44, 0x44, 0x11, 0x11, 0x44, 0x44,
0x11, 0x11, 0x44, 0x44, 0x11, 0x11, 0x44, 0x44,
0x55, 0x55, 0xaa, 0xaa, 0x55, 0x55, 0xaa, 0xaa,
0x55, 0x55, 0xaa, 0xaa, 0x55, 0x55, 0xaa, 0xaa,
0xee, 0xee, 0xbb, 0xbb, 0xee, 0xee, 0xbb, 0xbb,
0xee, 0xee, 0xbb, 0xbb, 0xee, 0xee, 0xbb, 0xbb,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8,
0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0xf8, 0xf8, 0x18,
0x18, 0xf8, 0xf8, 0x18, 0x18, 0x18, 0x18, 0x18,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xe6,
0xe6, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xfe,
0xfe, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0x00, 0x00, 0x00, 0xf8, 0xf8, 0x18,
0x18, 0xf8, 0xf8, 0x18, 0x18, 0x18, 0x18, 0x18,
0x66, 0x66, 0x66, 0x66, 0x66, 0xe6, 0xe6, 0x06,
0x06, 0xe6, 0xe6, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0x00, 0x00, 0x00, 0xfe, 0xfe, 0x06,
0x06, 0xe6, 0xe6, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0xe6, 0xe6, 0x06,
0x06, 0xfe, 0xfe, 0x00, 0x00, 0x00, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xfe,
0xfe, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0xf8, 0xf8, 0x18,
0x18, 0xf8, 0xf8, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xf8,
0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f,
0x1f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff,
0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff,
0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f,
0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff,
0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff,
0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x1f, 0x1f, 0x18,
0x18, 0x1f, 0x1f, 0x18, 0x18, 0x18, 0x18, 0x18,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x67,
0x67, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x67, 0x67, 0x60,
0x60, 0x7f, 0x7f, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x7f, 0x7f, 0x60,
0x60, 0x67, 0x67, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0xe7, 0xe7, 0x00,
0x00, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0x00,
0x00, 0xe7, 0xe7, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x67, 0x67, 0x60,
0x60, 0x67, 0x67, 0x66, 0x66, 0x66, 0x66, 0x66,
0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0x00,
0x00, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0xe7, 0xe7, 0x00,
0x00, 0xe7, 0xe7, 0x66, 0x66, 0x66, 0x66, 0x66,
0x18, 0x18, 0x18, 0x18, 0x18, 0xff, 0xff, 0x00,
0x00, 0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xff,
0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff, 0x00,
0x00, 0xff, 0xff, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff,
0xff, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x7f,
0x7f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x18, 0x18, 0x18, 0x18, 0x1f, 0x1f, 0x18,
0x18, 0x1f, 0x1f, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x1f, 0x1f, 0x18,
0x18, 0x1f, 0x1f, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x7f,
0x7f, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0xff,
0xff, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66, 0x66,
0x18, 0x18, 0x18, 0x18, 0x18, 0xff, 0xff, 0x18,
0x18, 0xff, 0xff, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8,
0xf8, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x1f,
0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0, 0xf0,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0xcc, 0xcc, 0xcc, 0xcc, 0x33, 0x33, 0x33, 0x33,
0xff, 0xff, 0xfe, 0xfe, 0xfc, 0xfc, 0xf8, 0xf8,
0xf0, 0xf0, 0xe0, 0xe0, 0xc0, 0xc0, 0x80, 0x80,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03, 0x03,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f,
0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f, 0x0f,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x1f,
0x1f, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xf8,
0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0xff,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x1f,
0x1f, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xff,
0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff,
0xff, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0xf8,
0xf8, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18, 0x18,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0, 0xc0,
0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0,
0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0, 0xe0,
0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07,
0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07, 0x07,
0xff, 0xff, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x18,
0x18, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x18, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x03, 0x03, 0x06, 0x06, 0x6c, 0x6c,
0x78, 0x78, 0x70, 0x70, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x7c, 0x7c, 0x7c,
0x7c, 0x7c, 0x7c, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00
};
/* ------------------------------------------------------------------------- */
/* Conversion tables. */
/* PETSCII lowercase/uppercase to extended ASCII converter table (used when
the C64 character set is on). */
BYTE cbm_petscii_business_to_charset[0x100] = {
0x40, 0x61, 0x62, 0x63, 0x64, 0x65, 0x66, 0x67,
0x68, 0x69, 0x6A, 0x6B, 0x6C, 0x6D, 0x6E, 0x6F,
0x70, 0x71, 0x72, 0x73, 0x74, 0x75, 0x76, 0x77,
0x78, 0x79, 0x7A, 0x5B, 0xA9, 0x5D, 0x18, 0x1B,
0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x26, 0x27,
0x28, 0x29, 0x2A, 0x2B, 0x2C, 0x2D, 0x2E, 0x2F,
0x30, 0x31, 0x32, 0x33, 0x34, 0x35, 0x36, 0x37,
0x38, 0x39, 0x3A, 0x3B, 0x3C, 0x3D, 0x3E, 0x3F,
0x40, 0x61, 0x62, 0x63, 0x64, 0x65, 0x66, 0x67,
0x68, 0x69, 0x6A, 0x6B, 0x6C, 0x6D, 0x6E, 0x6F,
0x70, 0x71, 0x72, 0x73, 0x74, 0x75, 0x76, 0x77,
0x78, 0x79, 0x7A, 0x5B, 0xA9, 0x5D, 0x18, 0x1B,
0x80, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x9B, 0x9C, 0x9D, 0xAA, 0xAB,
0x80, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x9B, 0x9C, 0x9D, 0xAA, 0xAB,
0xE0, 0xE1, 0xE2, 0xE3, 0xE4, 0xE5, 0xE6, 0xE7,
0xE8, 0xAC, 0xEA, 0xEB, 0xEC, 0xED, 0xEE, 0xEF,
0xF0, 0xF1, 0xF2, 0xF3, 0xF4, 0xF5, 0xF6, 0xF7,
0xA0, 0xA1, 0xFB, 0xA3, 0xA4, 0xA5, 0xA6, 0xA7,
0x80, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x9B, 0x9C, 0x9D, 0xAA, 0xAB,
0xE0, 0xE1, 0xE2, 0xE3, 0xE4, 0xE5, 0xE6, 0xE7,
0xE8, 0xAC, 0xEA, 0xEB, 0xEC, 0xED, 0xEE, 0xEF,
0xF0, 0xF1, 0xF2, 0xF3, 0xF4, 0xF5, 0xF6, 0xF7,
0xA0, 0xA1, 0xFB, 0xA3, 0xA4, 0xA5, 0xA6, 0xAA
};
/* PETSCII uppercase/graphics to extended ASCII converter table (used when the
C64 character set is on). */
BYTE cbm_petscii_graphics_to_charset[0x100] = {
0x40, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x5B, 0xA9, 0x5D, 0x18, 0x1B,
0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x26, 0x27,
0x28, 0x29, 0x2A, 0x2B, 0x2C, 0x2D, 0x2E, 0x2F,
0x30, 0x31, 0x32, 0x33, 0x34, 0x35, 0x36, 0x37,
0x38, 0x39, 0x3A, 0x3B, 0x3C, 0x3D, 0x3E, 0x3F,
0x40, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x5B, 0xA9, 0x5D, 0x18, 0x1B,
0x80, 0x81, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87,
0x88, 0x89, 0x8A, 0x8B, 0x8C, 0x8D, 0x8E, 0x8F,
0x90, 0x91, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97,
0x98, 0x99, 0x9A, 0x9B, 0x9C, 0x9D, 0x9E, 0x9F,
0x80, 0x81, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87,
0x88, 0x89, 0x8A, 0x8B, 0x8C, 0x8D, 0x8E, 0x8F,
0x90, 0x91, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97,
0x98, 0x99, 0x9A, 0x9B, 0x9C, 0x9D, 0x9E, 0x9F,
0xE0, 0xE1, 0xE2, 0xE3, 0xE4, 0xE5, 0xE6, 0xE7,
0xE8, 0xE9, 0xEA, 0xEB, 0xEC, 0xED, 0xEE, 0xEF,
0xF0, 0xF1, 0xF2, 0xF3, 0xF4, 0xF5, 0xF6, 0xF7,
0xA0, 0xA1, 0xA2, 0xA3, 0xA4, 0xA5, 0xA6, 0xA7,
0x80, 0x81, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87,
0x88, 0x89, 0x8A, 0x8B, 0x8C, 0x8D, 0x8E, 0x8F,
0x90, 0x91, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97,
0x98, 0x99, 0x9A, 0x9B, 0x9C, 0x9D, 0x9E, 0x9F,
0xE0, 0xE1, 0xE2, 0xE3, 0xE4, 0xE5, 0xE6, 0xE7,
0xE8, 0xE9, 0xEA, 0xEB, 0xEC, 0xED, 0xEE, 0xEF,
0xF0, 0xF1, 0xF2, 0xF3, 0xF4, 0xF5, 0xF6, 0xF7,
0xA0, 0xA1, 0xA2, 0xA3, 0xA4, 0xA5, 0xA6, 0x9E
};
/* FIXME: These are currently unused. */
BYTE cbm_petscii_business_to_ascii[0x100] = {
0x40, 0x61, 0x62, 0x63, 0x64, 0x65, 0x66, 0x67,
0x68, 0x69, 0x6A, 0x6B, 0x6C, 0x6D, 0x6E, 0x6F,
0x70, 0x71, 0x72, 0x73, 0x74, 0x75, 0x76, 0x77,
0x78, 0x79, 0x7A, 0x5B, 0x9C, 0x5D, 0x18, 0x1B,
0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x26, 0x27,
0x28, 0x29, 0x2A, 0x2B, 0x2C, 0x2D, 0x2E, 0x2F,
0x30, 0x31, 0x32, 0x33, 0x34, 0x35, 0x36, 0x37,
0x38, 0x39, 0x3A, 0x3B, 0x3C, 0x3D, 0x3E, 0x3F,
0x40, 0x61, 0x62, 0x63, 0x64, 0x65, 0x66, 0x67,
0x68, 0x69, 0x6A, 0x6B, 0x6C, 0x6D, 0x6E, 0x6F,
0x70, 0x71, 0x72, 0x73, 0x74, 0x75, 0x76, 0x77,
0x78, 0x79, 0x7A, 0x5B, 0x9C, 0x5D, 0x18, 0x1B,
0xC4, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0xC5, 0xF9, 0xB3, 0xF9, 0xF9,
0xC4, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0xC5, 0xF9, 0xB3, 0xF9, 0xF9,
0x5F, 0xDD, 0xDC, 0xC4, 0xC4, 0xB3, 0xF9, 0xB3,
0xF9, 0xF9, 0xB3, 0xC3, 0xF9, 0xC0, 0xBF, 0xC4,
0xDA, 0xC1, 0xC2, 0xB4, 0xB3, 0xDD, 0xDE, 0xC4,
0xDF, 0xDC, 0xFB, 0xF9, 0xF9, 0xD9, 0xF9, 0xF9,
0xC4, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0xC5, 0xF9, 0xB3, 0xF9, 0xF9,
0x5F, 0xDD, 0xDC, 0xC4, 0xC4, 0xB3, 0xF9, 0xB3,
0xF9, 0xF9, 0xB3, 0xC3, 0xF9, 0xC0, 0xBF, 0xC4,
0xDA, 0xC1, 0xC2, 0xB4, 0xB3, 0xDD, 0xDE, 0xC4,
0xDF, 0xDC, 0xFB, 0xF9, 0xF9, 0xD9, 0xF9, 0xF9
};
BYTE cbm_petscii_graphics_to_ascii[0x100] = {
0x40, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x5B, 0x9C, 0x5D, 0x18, 0x1B,
0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x26, 0x27,
0x28, 0x29, 0x2A, 0x2B, 0x2C, 0x2D, 0x2E, 0x2F,
0x30, 0x31, 0x32, 0x33, 0x34, 0x35, 0x36, 0x37,
0x38, 0x39, 0x3A, 0x3B, 0x3C, 0x3D, 0x3E, 0x3F,
0x40, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x5B, 0x9C, 0x5D, 0x18, 0x1B,
0xC4, 0x06, 0xB3, 0xC4, 0xC4, 0xC4, 0xC4, 0xB3,
0xB3, 0xBF, 0xC0, 0xD9, 0xC0, 0x5C, 0x2F, 0xDA,
0xBF, 0x07, 0xC4, 0x03, 0xB3, 0xDA, 0x58, 0x09,
0x05, 0xB3, 0x04, 0xC5, 0xF9, 0xB3, 0xE3, 0xF9,
0xC4, 0x06, 0xB3, 0xC4, 0xC4, 0xC4, 0xC4, 0xB3,
0xB3, 0xBF, 0xC0, 0xD9, 0xC0, 0x5C, 0x2F, 0xDA,
0xBF, 0x07, 0xC4, 0x03, 0xB3, 0xDA, 0x58, 0x09,
0x05, 0xB3, 0x04, 0xC5, 0xF9, 0xB3, 0xE3, 0xF9,
0x5F, 0xDD, 0xDC, 0xC4, 0xC4, 0xB3, 0xF9, 0xB3,
0xF9, 0xF9, 0xB3, 0xC3, 0xF9, 0xC0, 0xBF, 0xC4,
0xDA, 0xC1, 0xC2, 0xB4, 0xB3, 0xDD, 0xDE, 0xC4,
0xDF, 0xDC, 0xD9, 0xF9, 0xF9, 0xD9, 0xF9, 0xF9,
0xC4, 0x06, 0xB3, 0xC4, 0xC4, 0xC4, 0xC4, 0xB3,
0xB3, 0xBF, 0xC0, 0xD9, 0xC0, 0x5C, 0x2F, 0xDA,
0xBF, 0x07, 0xC4, 0x03, 0xB3, 0xDA, 0x58, 0x09,
0x05, 0xB3, 0x04, 0xC5, 0xF9, 0xB3, 0xE3, 0xF9,
0x5F, 0xDD, 0xDC, 0xC4, 0xC4, 0xB3, 0xF9, 0xB3,
0xF9, 0xF9, 0xB3, 0xC3, 0xF9, 0xC0, 0xBF, 0xC4,
0xDA, 0xC1, 0xC2, 0xB4, 0xB3, 0xDD, 0xDE, 0xC4,
0xDF, 0xDC, 0xD9, 0xF9, 0xF9, 0xD9, 0xF9, 0xE3
};
BYTE cbm_ascii_to_petscii[0x100] = {
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x21, 0x22, 0x23, 0x24, 0x25, 0x26, 0x27,
0x28, 0x29, 0x2A, 0x2B, 0x2C, 0x2D, 0x2E, 0x2F,
0x30, 0x31, 0x32, 0x33, 0x34, 0x35, 0x36, 0x37,
0x38, 0x39, 0x3A, 0x3B, 0x3C, 0x3D, 0x3E, 0x3F,
0x40, 0xC1, 0xC2, 0xC3, 0xC4, 0xC5, 0xC6, 0xC7,
0xC8, 0xC9, 0xCA, 0xCB, 0xCC, 0xCD, 0xCE, 0xCF,
0xD0, 0xD1, 0xD2, 0xD3, 0xD4, 0xD5, 0xD6, 0xD7,
0xD8, 0xD9, 0xDA, 0x5B, 0xCD, 0x5D, 0x5E, 0xA0,
0x20, 0x41, 0x42, 0x43, 0x44, 0x45, 0x46, 0x47,
0x48, 0x49, 0x4A, 0x4B, 0x4C, 0x4D, 0x4E, 0x4F,
0x50, 0x51, 0x52, 0x53, 0x54, 0x55, 0x56, 0x57,
0x58, 0x59, 0x5A, 0x5B, 0xDD, 0x5D, 0x2D, 0x20,
0xC3, 0x55, 0x45, 0x41, 0x41, 0x41, 0x41, 0x43,
0x45, 0x45, 0x45, 0x49, 0x49, 0x49, 0xC1, 0xC1,
0xC5, 0x41, 0xC1, 0x4F, 0x4F, 0x4F, 0x55, 0x55,
0x59, 0xCF, 0xD5, 0x43, 0x5C, 0xD9, 0x20, 0x20,
0x41, 0x45, 0x4F, 0x55, 0x4E, 0xCE, 0x20, 0x20,
0x3F, 0x20, 0x20, 0x20, 0x20, 0x21, 0x20, 0x20,
0xA6, 0xA6, 0xA6, 0xDD, 0xB3, 0xB3, 0xB3, 0xAE,
0xAE, 0xB3, 0xA6, 0xAE, 0xBD, 0xBD, 0xBD, 0xAE,
0xAD, 0xB1, 0xB2, 0xAB, 0xC0, 0xDB, 0xAB, 0xAB,
0xAD, 0xB0, 0xB1, 0xB2, 0xAB, 0xC0, 0xDB, 0xB1,
0xB1, 0xB2, 0xB2, 0xAD, 0xAD, 0xB0, 0xB0, 0xDB,
0xDB, 0xBD, 0xB0, 0x20, 0xA2, 0xA1, 0xB6, 0xB9,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20,
0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20, 0x20
};
|
trolleksii/kafka-ui | kafka-ui-e2e-checks/src/test/java/com/provectus/kafka/ui/pages/Pages.java | <gh_stars>1000+
package com.provectus.kafka.ui.pages;
public class Pages {
public static Pages INSTANCE = new Pages();
public MainPage mainPage = new MainPage();
public TopicsList topicsList = new TopicsList();
public TopicView topicView = new TopicView();
public ConnectorsList connectorsList = new ConnectorsList();
public ConnectorsView connectorsView = new ConnectorsView();
public MainPage open() {
return openMainPage();
}
public MainPage openMainPage() {
return mainPage.goTo();
}
public TopicsList openTopicsList(String clusterName) {
return topicsList.goTo(clusterName);
}
public TopicView openTopicView(String clusterName, String topicName) {
return topicView.goTo(clusterName, topicName);
}
public ConnectorsList openConnectorsList(String clusterName) {
return connectorsList.goTo(clusterName);
}
public ConnectorsView openConnectorsView(String clusterName, String connectorName) {
return connectorsView.goTo(clusterName, connectorName);
}
}
|
vishal230400/Coding-Solutions | src/com/vishal/codeforces/Q339/Q339A/Solution339A.java | package com.vishal.codeforces.Q339.Q339A;
import java.util.*;
import static java.lang.String.valueOf;
public class Solution339A {
public static void main(String[] args) {
Scanner sc = new Scanner(System.in);
String str = sc.next();
char[]a=str.replace("+","").toCharArray();
Arrays.sort(a);
String b=valueOf(a).replaceAll("(?i)([0-9])","$1+");
System.out.println(b.substring(0,b.length()-1));
sc.close();
}
} |
CogRob/TritonBot | cogrob_ros/speak_text_logging/src/speak_text_logger_node.cc | <gh_stars>1-10
// Copyright (c) 2018, The Regents of the University of California
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of the University of California nor the
// names of its contributors may be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
// BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
#include <memory>
#include "absl/memory/memory.h"
#include "cogrob/universal_logger/universal_logger.h"
#include "cogrob/universal_logger/universal_logger_flusher.h"
#include "cogrob/universal_logger/universal_logger_interface.h"
#include "ros/ros.h"
#include "speak_text_msgs/SpeakTextActionGoal.h"
#include "speak_text_msgs/SpeakTextActionResult.h"
#include "third_party/gflags.h"
#include "third_party/glog.h"
#include "speak_text_logger.h"
using speak_text_logging::SpeakTextLogger;
using cogrob::universal_logger::UniversalLogger;
using cogrob::universal_logger::UniversalLoggerFlusher;
using cogrob::universal_logger::UniversalLoggerInterface;
int main(int argc, char* argv[]) {
google::InitGoogleLogging(argv[0]);
gflags::ParseCommandLineFlags(&argc, &argv, true);
ros::init(argc, argv, "speak_text_logger_node");
UniversalLoggerFlusher logger_flusher;
auto universal_logger =
absl::make_unique<UniversalLogger>("dialogue/robot_speech");
CHECK_OK(universal_logger->RegisterWithFlusher(&logger_flusher));
SpeakTextLogger speak_text_logger(std::move(universal_logger));
ros::NodeHandle ros_node;
auto goal_callback = [&speak_text_logger] (
const speak_text_msgs::SpeakTextActionGoal::ConstPtr& msg) {
speak_text_logger.ActionGoalCallback(msg);
};
ros::Subscriber goal_sub =
ros_node.subscribe<speak_text_msgs::SpeakTextActionGoal>(
"/cogrob/speak_text_action/goal", 10, goal_callback);
auto result_callback = [&speak_text_logger] (
const speak_text_msgs::SpeakTextActionResult::ConstPtr& msg) {
speak_text_logger.ActionResultCallback(msg);
};
ros::Subscriber result_sub =
ros_node.subscribe<speak_text_msgs::SpeakTextActionResult>(
"/cogrob/speak_text_action/result", 10, result_callback);
ros::spin();
return 0;
}
|
akarnokd/akarnokd-misc | src/test/java/hu/akarnokd/rxjava2/TestMockitoCalls.java | package hu.akarnokd.rxjava2;
import static org.mockito.Mockito.*;
import java.util.List;
import org.junit.Test;
import io.reactivex.subjects.CompletableSubject;
public class TestMockitoCalls {
@Test
public void test() {
@SuppressWarnings("unchecked")
List<Integer> list = mock(List.class);
CompletableSubject source = CompletableSubject.create();
source.doOnSubscribe(v -> list.add(1))
.doOnError(e -> list.remove(1))
.doOnComplete(() -> list.remove(1))
.subscribe();
source.onComplete();
verify(list).add(1);
verify(list).remove(1);
verifyNoMoreInteractions(list);
}
}
|
g7401/pigeon | pigeon-gps/src/main/java/io/g740/pigeon/biz/object/dto/dictionary/UpdateDictionaryBuildProcessDefDto.java | package io.g740.pigeon.biz.object.dto.dictionary;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import io.g740.pigeon.biz.object.dto.general.SqlBuildStrategyContentDto;
import io.g740.pigeon.biz.object.dto.serialization.DictionaryBuildStrategyTypeEnumDeserializer;
import io.g740.pigeon.biz.object.dto.serialization.ScheduleTypeEnumJsonDeserializer;
import io.g740.pigeon.biz.share.constants.DictionaryBuildStrategyTypeEnum;
import io.g740.pigeon.biz.share.constants.ScheduleTypeEnum;
import lombok.Data;
/**
* @author bbottong
*/
@Data
public class UpdateDictionaryBuildProcessDefDto {
private Long uid;
/**
* 是否启用该流程
*/
private Boolean enabled;
/**
* 流程调度类型
*/
@JsonDeserialize(using = ScheduleTypeEnumJsonDeserializer.class)
private ScheduleTypeEnum scheduleType;
/**
* 流程调度明细
*/
private String scheduleTypeExtDetails;
/**
* 构建策略类型
*/
@JsonDeserialize(using = DictionaryBuildStrategyTypeEnumDeserializer.class)
private DictionaryBuildStrategyTypeEnum buildStrategyType;
/**
* SQL构建策略内容
*/
private SqlBuildStrategyContentDto sqlBuildStrategyContent;
/**
* 指定字典类目的UID
*/
private Long dictionaryCategoryUid;
}
|
zzzhr1990/common-grpc | go/services/tickets/tickets/tickets.pb.go | <filename>go/services/tickets/tickets/tickets.pb.go<gh_stars>0
// Code generated by protoc-gen-go. DO NOT EDIT.
// versions:
// protoc-gen-go v1.26.0
// protoc v3.15.5
// source: tickets/tickets.proto
package tickets
import (
common "github.com/zzzhr1990/common-grpc/go/common"
protoreflect "google.golang.org/protobuf/reflect/protoreflect"
protoimpl "google.golang.org/protobuf/runtime/protoimpl"
reflect "reflect"
sync "sync"
)
const (
// Verify that this generated code is sufficiently up-to-date.
_ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion)
// Verify that runtime/protoimpl is sufficiently up-to-date.
_ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20)
)
type Ticket struct {
state protoimpl.MessageState
sizeCache protoimpl.SizeCache
unknownFields protoimpl.UnknownFields
Identity int64 `protobuf:"varint,1,opt,name=identity,proto3" json:"identity,omitempty"`
UserIdentity int64 `protobuf:"varint,2,opt,name=user_identity,json=userIdentity,proto3" json:"user_identity,omitempty"`
Title string `protobuf:"bytes,3,opt,name=title,proto3" json:"title,omitempty"`
ReplyUserIdentity int64 `protobuf:"varint,4,opt,name=reply_user_identity,json=replyUserIdentity,proto3" json:"reply_user_identity,omitempty"`
Type int32 `protobuf:"varint,5,opt,name=type,proto3" json:"type,omitempty"`
Status int32 `protobuf:"varint,6,opt,name=status,proto3" json:"status,omitempty"`
CreateTime int64 `protobuf:"varint,7,opt,name=create_time,json=createTime,proto3" json:"create_time,omitempty"`
RefreshTime int64 `protobuf:"varint,8,opt,name=refresh_time,json=refreshTime,proto3" json:"refresh_time,omitempty"`
Message string `protobuf:"bytes,9,opt,name=message,proto3" json:"message,omitempty"`
Images string `protobuf:"bytes,10,opt,name=images,proto3" json:"images,omitempty"`
}
func (x *Ticket) Reset() {
*x = Ticket{}
if protoimpl.UnsafeEnabled {
mi := &file_tickets_tickets_proto_msgTypes[0]
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
ms.StoreMessageInfo(mi)
}
}
func (x *Ticket) String() string {
return protoimpl.X.MessageStringOf(x)
}
func (*Ticket) ProtoMessage() {}
func (x *Ticket) ProtoReflect() protoreflect.Message {
mi := &file_tickets_tickets_proto_msgTypes[0]
if protoimpl.UnsafeEnabled && x != nil {
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
if ms.LoadMessageInfo() == nil {
ms.StoreMessageInfo(mi)
}
return ms
}
return mi.MessageOf(x)
}
// Deprecated: Use Ticket.ProtoReflect.Descriptor instead.
func (*Ticket) Descriptor() ([]byte, []int) {
return file_tickets_tickets_proto_rawDescGZIP(), []int{0}
}
func (x *Ticket) GetIdentity() int64 {
if x != nil {
return x.Identity
}
return 0
}
func (x *Ticket) GetUserIdentity() int64 {
if x != nil {
return x.UserIdentity
}
return 0
}
func (x *Ticket) GetTitle() string {
if x != nil {
return x.Title
}
return ""
}
func (x *Ticket) GetReplyUserIdentity() int64 {
if x != nil {
return x.ReplyUserIdentity
}
return 0
}
func (x *Ticket) GetType() int32 {
if x != nil {
return x.Type
}
return 0
}
func (x *Ticket) GetStatus() int32 {
if x != nil {
return x.Status
}
return 0
}
func (x *Ticket) GetCreateTime() int64 {
if x != nil {
return x.CreateTime
}
return 0
}
func (x *Ticket) GetRefreshTime() int64 {
if x != nil {
return x.RefreshTime
}
return 0
}
func (x *Ticket) GetMessage() string {
if x != nil {
return x.Message
}
return ""
}
func (x *Ticket) GetImages() string {
if x != nil {
return x.Images
}
return ""
}
type Reply struct {
state protoimpl.MessageState
sizeCache protoimpl.SizeCache
unknownFields protoimpl.UnknownFields
Identity int64 `protobuf:"varint,1,opt,name=identity,proto3" json:"identity,omitempty"`
UserIdentity int64 `protobuf:"varint,2,opt,name=user_identity,json=userIdentity,proto3" json:"user_identity,omitempty"`
TicketIdentity int64 `protobuf:"varint,4,opt,name=ticket_identity,json=ticketIdentity,proto3" json:"ticket_identity,omitempty"`
// int32 type = 5;
// int32 status = 6;
CreateTime int64 `protobuf:"varint,7,opt,name=create_time,json=createTime,proto3" json:"create_time,omitempty"`
// string create_address = 8;
Message string `protobuf:"bytes,9,opt,name=message,proto3" json:"message,omitempty"`
Images string `protobuf:"bytes,10,opt,name=images,proto3" json:"images,omitempty"`
}
func (x *Reply) Reset() {
*x = Reply{}
if protoimpl.UnsafeEnabled {
mi := &file_tickets_tickets_proto_msgTypes[1]
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
ms.StoreMessageInfo(mi)
}
}
func (x *Reply) String() string {
return protoimpl.X.MessageStringOf(x)
}
func (*Reply) ProtoMessage() {}
func (x *Reply) ProtoReflect() protoreflect.Message {
mi := &file_tickets_tickets_proto_msgTypes[1]
if protoimpl.UnsafeEnabled && x != nil {
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
if ms.LoadMessageInfo() == nil {
ms.StoreMessageInfo(mi)
}
return ms
}
return mi.MessageOf(x)
}
// Deprecated: Use Reply.ProtoReflect.Descriptor instead.
func (*Reply) Descriptor() ([]byte, []int) {
return file_tickets_tickets_proto_rawDescGZIP(), []int{1}
}
func (x *Reply) GetIdentity() int64 {
if x != nil {
return x.Identity
}
return 0
}
func (x *Reply) GetUserIdentity() int64 {
if x != nil {
return x.UserIdentity
}
return 0
}
func (x *Reply) GetTicketIdentity() int64 {
if x != nil {
return x.TicketIdentity
}
return 0
}
func (x *Reply) GetCreateTime() int64 {
if x != nil {
return x.CreateTime
}
return 0
}
func (x *Reply) GetMessage() string {
if x != nil {
return x.Message
}
return ""
}
func (x *Reply) GetImages() string {
if x != nil {
return x.Images
}
return ""
}
type TicketListRequest struct {
state protoimpl.MessageState
sizeCache protoimpl.SizeCache
unknownFields protoimpl.UnknownFields
UserIdentity int64 `protobuf:"varint,2,opt,name=user_identity,json=userIdentity,proto3" json:"user_identity,omitempty"`
// string path = 3;
ListInfo *common.ListInfo `protobuf:"bytes,4,opt,name=list_info,json=listInfo,proto3" json:"list_info,omitempty"`
OrderBy []*common.OrderByRequest `protobuf:"bytes,5,rep,name=order_by,json=orderBy,proto3" json:"order_by,omitempty"` // OrderFilterRequest filter = 6;
}
func (x *TicketListRequest) Reset() {
*x = TicketListRequest{}
if protoimpl.UnsafeEnabled {
mi := &file_tickets_tickets_proto_msgTypes[2]
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
ms.StoreMessageInfo(mi)
}
}
func (x *TicketListRequest) String() string {
return protoimpl.X.MessageStringOf(x)
}
func (*TicketListRequest) ProtoMessage() {}
func (x *TicketListRequest) ProtoReflect() protoreflect.Message {
mi := &file_tickets_tickets_proto_msgTypes[2]
if protoimpl.UnsafeEnabled && x != nil {
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
if ms.LoadMessageInfo() == nil {
ms.StoreMessageInfo(mi)
}
return ms
}
return mi.MessageOf(x)
}
// Deprecated: Use TicketListRequest.ProtoReflect.Descriptor instead.
func (*TicketListRequest) Descriptor() ([]byte, []int) {
return file_tickets_tickets_proto_rawDescGZIP(), []int{2}
}
func (x *TicketListRequest) GetUserIdentity() int64 {
if x != nil {
return x.UserIdentity
}
return 0
}
func (x *TicketListRequest) GetListInfo() *common.ListInfo {
if x != nil {
return x.ListInfo
}
return nil
}
func (x *TicketListRequest) GetOrderBy() []*common.OrderByRequest {
if x != nil {
return x.OrderBy
}
return nil
}
type ReplyListRequest struct {
state protoimpl.MessageState
sizeCache protoimpl.SizeCache
unknownFields protoimpl.UnknownFields
TicketIdentity int64 `protobuf:"varint,1,opt,name=ticket_identity,json=ticketIdentity,proto3" json:"ticket_identity,omitempty"`
UserIdentity int64 `protobuf:"varint,2,opt,name=user_identity,json=userIdentity,proto3" json:"user_identity,omitempty"`
// string path = 3;
ListInfo *common.ListInfo `protobuf:"bytes,4,opt,name=list_info,json=listInfo,proto3" json:"list_info,omitempty"`
OrderBy []*common.OrderByRequest `protobuf:"bytes,5,rep,name=order_by,json=orderBy,proto3" json:"order_by,omitempty"` // OrderFilterRequest filter = 6;
}
func (x *ReplyListRequest) Reset() {
*x = ReplyListRequest{}
if protoimpl.UnsafeEnabled {
mi := &file_tickets_tickets_proto_msgTypes[3]
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
ms.StoreMessageInfo(mi)
}
}
func (x *ReplyListRequest) String() string {
return protoimpl.X.MessageStringOf(x)
}
func (*ReplyListRequest) ProtoMessage() {}
func (x *ReplyListRequest) ProtoReflect() protoreflect.Message {
mi := &file_tickets_tickets_proto_msgTypes[3]
if protoimpl.UnsafeEnabled && x != nil {
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
if ms.LoadMessageInfo() == nil {
ms.StoreMessageInfo(mi)
}
return ms
}
return mi.MessageOf(x)
}
// Deprecated: Use ReplyListRequest.ProtoReflect.Descriptor instead.
func (*ReplyListRequest) Descriptor() ([]byte, []int) {
return file_tickets_tickets_proto_rawDescGZIP(), []int{3}
}
func (x *ReplyListRequest) GetTicketIdentity() int64 {
if x != nil {
return x.TicketIdentity
}
return 0
}
func (x *ReplyListRequest) GetUserIdentity() int64 {
if x != nil {
return x.UserIdentity
}
return 0
}
func (x *ReplyListRequest) GetListInfo() *common.ListInfo {
if x != nil {
return x.ListInfo
}
return nil
}
func (x *ReplyListRequest) GetOrderBy() []*common.OrderByRequest {
if x != nil {
return x.OrderBy
}
return nil
}
//
//message OrderFilterRequest {
//string identity = 1;
//int64 plan_type = 2;
//string path = 3;
//}
type TicketListResponse struct {
state protoimpl.MessageState
sizeCache protoimpl.SizeCache
unknownFields protoimpl.UnknownFields
Data []*Ticket `protobuf:"bytes,1,rep,name=data,proto3" json:"data,omitempty"`
}
func (x *TicketListResponse) Reset() {
*x = TicketListResponse{}
if protoimpl.UnsafeEnabled {
mi := &file_tickets_tickets_proto_msgTypes[4]
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
ms.StoreMessageInfo(mi)
}
}
func (x *TicketListResponse) String() string {
return protoimpl.X.MessageStringOf(x)
}
func (*TicketListResponse) ProtoMessage() {}
func (x *TicketListResponse) ProtoReflect() protoreflect.Message {
mi := &file_tickets_tickets_proto_msgTypes[4]
if protoimpl.UnsafeEnabled && x != nil {
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
if ms.LoadMessageInfo() == nil {
ms.StoreMessageInfo(mi)
}
return ms
}
return mi.MessageOf(x)
}
// Deprecated: Use TicketListResponse.ProtoReflect.Descriptor instead.
func (*TicketListResponse) Descriptor() ([]byte, []int) {
return file_tickets_tickets_proto_rawDescGZIP(), []int{4}
}
func (x *TicketListResponse) GetData() []*Ticket {
if x != nil {
return x.Data
}
return nil
}
type ReplyListResponse struct {
state protoimpl.MessageState
sizeCache protoimpl.SizeCache
unknownFields protoimpl.UnknownFields
Ticket *Ticket `protobuf:"bytes,1,opt,name=Ticket,proto3" json:"Ticket,omitempty"`
Data []*Reply `protobuf:"bytes,2,rep,name=data,proto3" json:"data,omitempty"`
}
func (x *ReplyListResponse) Reset() {
*x = ReplyListResponse{}
if protoimpl.UnsafeEnabled {
mi := &file_tickets_tickets_proto_msgTypes[5]
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
ms.StoreMessageInfo(mi)
}
}
func (x *ReplyListResponse) String() string {
return protoimpl.X.MessageStringOf(x)
}
func (*ReplyListResponse) ProtoMessage() {}
func (x *ReplyListResponse) ProtoReflect() protoreflect.Message {
mi := &file_tickets_tickets_proto_msgTypes[5]
if protoimpl.UnsafeEnabled && x != nil {
ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
if ms.LoadMessageInfo() == nil {
ms.StoreMessageInfo(mi)
}
return ms
}
return mi.MessageOf(x)
}
// Deprecated: Use ReplyListResponse.ProtoReflect.Descriptor instead.
func (*ReplyListResponse) Descriptor() ([]byte, []int) {
return file_tickets_tickets_proto_rawDescGZIP(), []int{5}
}
func (x *ReplyListResponse) GetTicket() *Ticket {
if x != nil {
return x.Ticket
}
return nil
}
func (x *ReplyListResponse) GetData() []*Reply {
if x != nil {
return x.Data
}
return nil
}
var File_tickets_tickets_proto protoreflect.FileDescriptor
var file_tickets_tickets_proto_rawDesc = []byte{
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}
var (
file_tickets_tickets_proto_rawDescOnce sync.Once
file_tickets_tickets_proto_rawDescData = file_tickets_tickets_proto_rawDesc
)
func file_tickets_tickets_proto_rawDescGZIP() []byte {
file_tickets_tickets_proto_rawDescOnce.Do(func() {
file_tickets_tickets_proto_rawDescData = protoimpl.X.CompressGZIP(file_tickets_tickets_proto_rawDescData)
})
return file_tickets_tickets_proto_rawDescData
}
var file_tickets_tickets_proto_msgTypes = make([]protoimpl.MessageInfo, 6)
var file_tickets_tickets_proto_goTypes = []interface{}{
(*Ticket)(nil), // 0: services.Ticket
(*Reply)(nil), // 1: services.Reply
(*TicketListRequest)(nil), // 2: services.TicketListRequest
(*ReplyListRequest)(nil), // 3: services.ReplyListRequest
(*TicketListResponse)(nil), // 4: services.TicketListResponse
(*ReplyListResponse)(nil), // 5: services.ReplyListResponse
(*common.ListInfo)(nil), // 6: services.ListInfo
(*common.OrderByRequest)(nil), // 7: services.OrderByRequest
}
var file_tickets_tickets_proto_depIdxs = []int32{
6, // 0: services.TicketListRequest.list_info:type_name -> services.ListInfo
7, // 1: services.TicketListRequest.order_by:type_name -> services.OrderByRequest
6, // 2: services.ReplyListRequest.list_info:type_name -> services.ListInfo
7, // 3: services.ReplyListRequest.order_by:type_name -> services.OrderByRequest
0, // 4: services.TicketListResponse.data:type_name -> services.Ticket
0, // 5: services.ReplyListResponse.Ticket:type_name -> services.Ticket
1, // 6: services.ReplyListResponse.data:type_name -> services.Reply
0, // 7: services.TicketsService.Create:input_type -> services.Ticket
2, // 8: services.TicketsService.List:input_type -> services.TicketListRequest
3, // 9: services.TicketsService.ListReply:input_type -> services.ReplyListRequest
0, // 10: services.TicketsService.Get:input_type -> services.Ticket
1, // 11: services.TicketsService.GetReply:input_type -> services.Reply
1, // 12: services.TicketsService.ReplyTicket:input_type -> services.Reply
0, // 13: services.TicketsService.Close:input_type -> services.Ticket
0, // 14: services.TicketsService.Delete:input_type -> services.Ticket
1, // 15: services.TicketsService.DeleteReply:input_type -> services.Reply
0, // 16: services.TicketsService.Create:output_type -> services.Ticket
4, // 17: services.TicketsService.List:output_type -> services.TicketListResponse
5, // 18: services.TicketsService.ListReply:output_type -> services.ReplyListResponse
0, // 19: services.TicketsService.Get:output_type -> services.Ticket
1, // 20: services.TicketsService.GetReply:output_type -> services.Reply
1, // 21: services.TicketsService.ReplyTicket:output_type -> services.Reply
0, // 22: services.TicketsService.Close:output_type -> services.Ticket
0, // 23: services.TicketsService.Delete:output_type -> services.Ticket
1, // 24: services.TicketsService.DeleteReply:output_type -> services.Reply
16, // [16:25] is the sub-list for method output_type
7, // [7:16] is the sub-list for method input_type
7, // [7:7] is the sub-list for extension type_name
7, // [7:7] is the sub-list for extension extendee
0, // [0:7] is the sub-list for field type_name
}
func init() { file_tickets_tickets_proto_init() }
func file_tickets_tickets_proto_init() {
if File_tickets_tickets_proto != nil {
return
}
if !protoimpl.UnsafeEnabled {
file_tickets_tickets_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} {
switch v := v.(*Ticket); i {
case 0:
return &v.state
case 1:
return &v.sizeCache
case 2:
return &v.unknownFields
default:
return nil
}
}
file_tickets_tickets_proto_msgTypes[1].Exporter = func(v interface{}, i int) interface{} {
switch v := v.(*Reply); i {
case 0:
return &v.state
case 1:
return &v.sizeCache
case 2:
return &v.unknownFields
default:
return nil
}
}
file_tickets_tickets_proto_msgTypes[2].Exporter = func(v interface{}, i int) interface{} {
switch v := v.(*TicketListRequest); i {
case 0:
return &v.state
case 1:
return &v.sizeCache
case 2:
return &v.unknownFields
default:
return nil
}
}
file_tickets_tickets_proto_msgTypes[3].Exporter = func(v interface{}, i int) interface{} {
switch v := v.(*ReplyListRequest); i {
case 0:
return &v.state
case 1:
return &v.sizeCache
case 2:
return &v.unknownFields
default:
return nil
}
}
file_tickets_tickets_proto_msgTypes[4].Exporter = func(v interface{}, i int) interface{} {
switch v := v.(*TicketListResponse); i {
case 0:
return &v.state
case 1:
return &v.sizeCache
case 2:
return &v.unknownFields
default:
return nil
}
}
file_tickets_tickets_proto_msgTypes[5].Exporter = func(v interface{}, i int) interface{} {
switch v := v.(*ReplyListResponse); i {
case 0:
return &v.state
case 1:
return &v.sizeCache
case 2:
return &v.unknownFields
default:
return nil
}
}
}
type x struct{}
out := protoimpl.TypeBuilder{
File: protoimpl.DescBuilder{
GoPackagePath: reflect.TypeOf(x{}).PkgPath(),
RawDescriptor: file_tickets_tickets_proto_rawDesc,
NumEnums: 0,
NumMessages: 6,
NumExtensions: 0,
NumServices: 1,
},
GoTypes: file_tickets_tickets_proto_goTypes,
DependencyIndexes: file_tickets_tickets_proto_depIdxs,
MessageInfos: file_tickets_tickets_proto_msgTypes,
}.Build()
File_tickets_tickets_proto = out.File
file_tickets_tickets_proto_rawDesc = nil
file_tickets_tickets_proto_goTypes = nil
file_tickets_tickets_proto_depIdxs = nil
}
|
jamesmunns/nRF5-sdk | examples/ble_central_and_peripheral/experimental/ble_app_att_mtu_throughput/main.c | <reponame>jamesmunns/nRF5-sdk
/**
* Copyright (c) 2016 - 2017, Nordic Semiconductor ASA
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form, except as embedded into a Nordic
* Semiconductor ASA integrated circuit in a product or a software update for
* such product, must reproduce the above copyright notice, this list of
* conditions and the following disclaimer in the documentation and/or other
* materials provided with the distribution.
*
* 3. Neither the name of Nordic Semiconductor ASA nor the names of its
* contributors may be used to endorse or promote products derived from this
* software without specific prior written permission.
*
* 4. This software, with or without modification, must only be used with a
* Nordic Semiconductor ASA integrated circuit.
*
* 5. Any software provided in binary form under this license must not be reverse
* engineered, decompiled, modified and/or disassembled.
*
* THIS SOFTWARE IS PROVIDED BY NORDIC SEMICONDUCTOR ASA "AS IS" AND ANY EXPRESS
* OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY, NONINFRINGEMENT, AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL NORDIC SEMICONDUCTOR ASA OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
* GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
/**@cond To Make Doxygen skip documentation generation for this file.
* @{
*/
#include <stdbool.h>
#include <stdint.h>
#include <string.h>
#include <stdio.h>
#include "amt.h"
#include "counter.h"
#include "sdk_config.h"
#include "boards.h"
#include "bsp.h"
#include "bsp_btn_ble.h"
#include "nrf.h"
#include "ble.h"
#include "ble_hci.h"
#include "nordic_common.h"
#include "nrf_gpio.h"
#include "ble_advdata.h"
#include "ble_srv_common.h"
#include "softdevice_handler.h"
#include "nrf_ble_gatt.h"
#include "app_timer.h"
#include "app_error.h"
#include "ble_conn_params.h"
#define NRF_LOG_MODULE_NAME "APP"
#include "nrf_log.h"
#include "nrf_log_ctrl.h"
#define CONN_INTERVAL_DEFAULT (uint16_t)(MSEC_TO_UNITS(7.5, UNIT_1_25_MS)) /**< Default connection interval used at connection establishment by central side. */
#define CONN_INTERVAL_MIN (uint16_t)(MSEC_TO_UNITS(7.5, UNIT_1_25_MS)) /**< Minimum acceptable connection interval, in 1.25 ms units. */
#define CONN_INTERVAL_MAX (uint16_t)(MSEC_TO_UNITS(500, UNIT_1_25_MS)) /**< Maximum acceptable connection interval, in 1.25 ms units. */
#define CONN_SUP_TIMEOUT (uint16_t)(MSEC_TO_UNITS(4000, UNIT_10_MS)) /**< Connection supervisory timeout (4 seconds). */
#define SLAVE_LATENCY 0 /**< Slave latency. */
#define SCAN_ADV_LED BSP_BOARD_LED_0
#define READY_LED BSP_BOARD_LED_1
#define PROGRESS_LED BSP_BOARD_LED_2
#define DONE_LED BSP_BOARD_LED_3
#define YES 'y'
#define ONE '1'
#define TWO '2'
#define THREE '3'
#define FOUR '4'
#define ENTER '\r'
#define BOARD_TESTER_BUTTON BSP_BUTTON_2 /**< Button to press at beginning of the test to indicate that this board is connected to the PC and takes input from it via the UART. */
#define BOARD_DUMMY_BUTTON BSP_BUTTON_3 /**< Button to press at beginning of the test to indicate that this board is standalone (automatic behavior). */
#define BUTTON_DETECTION_DELAY APP_TIMER_TICKS(50) /**< Delay from a GPIOTE event until a button is reported as pushed (in number of timer ticks). */
#define LL_HEADER_LEN 4 /**< Link layer header length. */
#define CONN_CFG_TAG 1 /**< A tag that refers to the BLE stack configuration we set with @ref sd_ble_cfg_set. Default tag is @ref BLE_CONN_CFG_TAG_DEFAULT. */
#define FIRST_CONN_PARAMS_UPDATE_DELAY APP_TIMER_TICKS(500) /**< Time from initiating event (connect or start of notification) to first time sd_ble_gap_conn_param_update is called (0.5 seconds). */
#define NEXT_CONN_PARAMS_UPDATE_DELAY APP_TIMER_TICKS(500) /**< Time between each call to sd_ble_gap_conn_param_update after the first call (0.5 seconds). */
#define MAX_CONN_PARAMS_UPDATE_COUNT 2 /**< Number of attempts before giving up the connection parameter negotiation. */
typedef enum
{
NOT_SELECTED = 0x00,
BOARD_TESTER,
BOARD_DUMMY,
} board_role_t;
typedef struct
{
uint16_t att_mtu; /**< GATT ATT MTU, in bytes. */
uint16_t conn_interval; /**< Connection interval expressed in units of 1.25 ms. */
bool data_len_ext_enabled; /**< Data length extension status. */
bool conn_evt_len_ext_enabled; /**< Connection event length extension status. */
uint8_t rxtx_phy; /**< Preferred PHY. */
} test_params_t;
/**@brief Variable length data encapsulation in terms of length and pointer to data. */
typedef struct
{
uint8_t * p_data; /**< Pointer to data. */
uint16_t data_len; /**< Length of data. */
} data_t;
static nrf_ble_amtc_t m_amtc;
static nrf_ble_amts_t m_amts;
static board_role_t volatile m_board_role = NOT_SELECTED;
static bool volatile m_run_test;
static bool volatile m_print_menu;
static bool volatile m_notif_enabled;
static bool volatile m_mtu_exchanged;
static bool volatile m_data_length_updated;
#if defined(S140)
static bool volatile m_phy_updated;
#endif
static bool volatile m_conn_interval_configured;
static uint16_t m_conn_handle = BLE_CONN_HANDLE_INVALID; /**< Handle of the current BLE connection .*/
static uint8_t m_gap_role = BLE_GAP_ROLE_INVALID; /**< BLE role for this connection, see @ref BLE_GAP_ROLES */
static nrf_ble_gatt_t m_gatt; /**< GATT module instance. */
static ble_db_discovery_t m_ble_db_discovery; /**< DB discovery module instance. */
// Name to use for advertising and connection.
static char const m_target_periph_name[] = DEVICE_NAME;
// Test parameters.
// Settings like ATT MTU size are set only once on the dummy board.
// Make sure that defaults are sensible.
static test_params_t m_test_params =
{
.att_mtu = NRF_BLE_GATT_MAX_MTU_SIZE,
.conn_interval = CONN_INTERVAL_DEFAULT,
.data_len_ext_enabled = true,
.conn_evt_len_ext_enabled = true,
#if defined(S140)
.rxtx_phy = BLE_GAP_PHY_2MBPS | BLE_GAP_PHY_1MBPS | BLE_GAP_PHY_CODED,
#endif
};
// Scan parameters requested for scanning and connection.
static ble_gap_scan_params_t const m_scan_param =
{
.active = 0x00,
.interval = SCAN_INTERVAL,
.window = SCAN_WINDOW,
.use_whitelist = 0x00,
.adv_dir_report = 0x00,
.timeout = 0x0000, // No timeout.
};
// Connection parameters requested for connection.
static ble_gap_conn_params_t m_conn_param =
{
.min_conn_interval = CONN_INTERVAL_MIN, // Minimum connection interval.
.max_conn_interval = CONN_INTERVAL_MAX, // Maximum connection interval.
.slave_latency = SLAVE_LATENCY, // Slave latency.
.conn_sup_timeout = CONN_SUP_TIMEOUT // Supervisory timeout.
};
static void test_terminate(void);
#ifdef S140
static uint32_t phy_str(uint8_t phy)
{
static char const * str[] =
{
"1 Mbps",
"2 Mbps",
"Coded",
"Unknown"
};
switch (phy)
{
case BLE_GAP_PHY_1MBPS:
return (uint32_t)(str[0]);
case BLE_GAP_PHY_2MBPS:
case BLE_GAP_PHY_2MBPS | BLE_GAP_PHY_1MBPS:
case BLE_GAP_PHY_2MBPS | BLE_GAP_PHY_1MBPS | BLE_GAP_PHY_CODED:
return (uint32_t)(str[1]);
case BLE_GAP_PHY_CODED:
return (uint32_t)(str[2]);
default:
return (uint32_t)(str[3]);
}
}
#endif
/**@brief Parses advertisement data, providing length and location of the field in case
* matching data is found.
*
* @param[in] Type of data to be looked for in advertisement data.
* @param[in] Advertisement report length and pointer to report.
* @param[out] If data type requested is found in the data report, type data length and
* pointer to data will be populated here.
*
* @retval NRF_SUCCESS if the data type is found in the report.
* @retval NRF_ERROR_NOT_FOUND if the data type could not be found.
*/
static uint32_t adv_report_parse(uint8_t type, data_t * p_advdata, data_t * p_typedata)
{
uint32_t index = 0;
uint8_t * p_data;
p_data = p_advdata->p_data;
while (index < p_advdata->data_len)
{
uint8_t field_length = p_data[index];
uint8_t field_type = p_data[index + 1];
if (field_type == type)
{
p_typedata->p_data = &p_data[index + 2];
p_typedata->data_len = field_length - 1;
return NRF_SUCCESS;
}
index += field_length + 1;
}
return NRF_ERROR_NOT_FOUND;
}
/**@brief Function for searching a given name in the advertisement packets.
*
* @details Use this function to parse received advertising data and to find a given
* name in them either as 'complete_local_name' or as 'short_local_name'.
*
* @param[in] p_adv_report advertising data to parse.
* @param[in] name_to_find name to search.
* @return true if the given name was found, false otherwise.
*/
static bool find_adv_name(ble_gap_evt_adv_report_t const * p_adv_report, char const * name_to_find)
{
ret_code_t err_code;
data_t adv_data;
data_t dev_name;
bool found = false;
// Initialize advertisement report for parsing.
adv_data.p_data = (uint8_t *)p_adv_report->data;
adv_data.data_len = p_adv_report->dlen;
// Search for matching advertising names.
err_code = adv_report_parse(BLE_GAP_AD_TYPE_COMPLETE_LOCAL_NAME, &adv_data, &dev_name);
if ( (err_code == NRF_SUCCESS)
&& (strlen(name_to_find) == dev_name.data_len)
&& (memcmp(name_to_find, dev_name.p_data, dev_name.data_len) == 0))
{
found = true;
}
else
{
// Look for the short local name if the complete name was not found.
err_code = adv_report_parse(BLE_GAP_AD_TYPE_SHORT_LOCAL_NAME, &adv_data, &dev_name);
if ( (err_code == NRF_SUCCESS)
&& (strlen(name_to_find) == dev_name.data_len)
&& (memcmp(m_target_periph_name, dev_name.p_data, dev_name.data_len) == 0))
{
found = true;
}
}
return found;
}
/**@brief Function for handling BLE_GAP_ADV_REPORT events.
* Search for a peer with matching device name.
* If found, stop advertising and send a connection request to the peer.
*/
static void on_ble_gap_evt_adv_report(ble_gap_evt_t const * p_gap_evt)
{
if (!find_adv_name(&p_gap_evt->params.adv_report, m_target_periph_name))
{
return;
}
NRF_LOG_INFO("Device \"%s\" found, sending a connection request.\r\n",
(uint32_t) m_target_periph_name);
// Stop advertising.
(void) sd_ble_gap_adv_stop();
// Initiate connection.
m_conn_param.min_conn_interval = CONN_INTERVAL_DEFAULT;
m_conn_param.max_conn_interval = CONN_INTERVAL_DEFAULT;
ret_code_t err_code;
err_code = sd_ble_gap_connect(&p_gap_evt->params.adv_report.peer_addr,
&m_scan_param,
&m_conn_param,
CONN_CFG_TAG);
if (err_code != NRF_SUCCESS)
{
NRF_LOG_ERROR("sd_ble_gap_connect() failed: 0x%x.\r\n", err_code);
}
}
/**@brief Function for handling BLE_GAP_EVT_CONNECTED events.
* Save the connection handle and GAP role, then discover the peer DB.
*/
static void on_ble_gap_evt_connected(ble_gap_evt_t const * p_gap_evt)
{
m_conn_handle = p_gap_evt->conn_handle;
m_gap_role = p_gap_evt->params.connected.role;
if (m_gap_role == BLE_GAP_ROLE_PERIPH)
{
NRF_LOG_INFO("Connected as a peripheral.\r\n");
}
else if (m_gap_role == BLE_GAP_ROLE_CENTRAL)
{
NRF_LOG_INFO("Connected as a central.\r\n");
}
// Stop scanning and advertising.
(void) sd_ble_gap_scan_stop();
(void) sd_ble_gap_adv_stop();
NRF_LOG_INFO("Discovering GATT database...\r\n");
// Zero the database before starting discovery.
memset(&m_ble_db_discovery, 0x00, sizeof(m_ble_db_discovery));
ret_code_t err_code;
err_code = ble_db_discovery_start(&m_ble_db_discovery, p_gap_evt->conn_handle);
APP_ERROR_CHECK(err_code);
#if defined(S140)
// Request PHY.
ble_gap_phys_t phys =
{
.tx_phys = m_test_params.rxtx_phy,
.rx_phys = m_test_params.rxtx_phy,
};
err_code = sd_ble_gap_phy_request(p_gap_evt->conn_handle, &phys);
APP_ERROR_CHECK(err_code);
#endif
bsp_board_leds_off();
}
/**@brief Function for handling BLE_GAP_EVT_DISCONNECTED events.
* Unset the connection handle and terminate the test.
*/
static void on_ble_gap_evt_disconnected(ble_gap_evt_t const * p_gap_evt)
{
m_conn_handle = BLE_CONN_HANDLE_INVALID;
NRF_LOG_DEBUG("Disconnected: reason 0x%x.\r\n", p_gap_evt->params.disconnected.reason);
if (m_run_test)
{
NRF_LOG_WARNING("GAP disconnection event received while test was running.\r\n")
}
bsp_board_leds_off();
test_terminate();
}
/**@brief Function for handling BLE Stack events.
*
* @param[in] p_ble_evt Bluetooth stack event.
*/
static void on_ble_evt(ble_evt_t * p_ble_evt)
{
uint32_t err_code;
ble_gap_evt_t const * p_gap_evt = &p_ble_evt->evt.gap_evt;
switch (p_ble_evt->header.evt_id)
{
case BLE_GAP_EVT_ADV_REPORT:
on_ble_gap_evt_adv_report(p_gap_evt);
break;
case BLE_GAP_EVT_CONNECTED:
on_ble_gap_evt_connected(p_gap_evt);
break;
case BLE_GAP_EVT_DISCONNECTED:
on_ble_gap_evt_disconnected(p_gap_evt);
break;
case BLE_GAP_EVT_CONN_PARAM_UPDATE_REQUEST:
{
// Accept parameters requested by the peer.
ble_gap_conn_params_t params;
params = p_gap_evt->params.conn_param_update_request.conn_params;
params.max_conn_interval = params.min_conn_interval;
err_code = sd_ble_gap_conn_param_update(p_gap_evt->conn_handle, ¶ms);
APP_ERROR_CHECK(err_code);
} break;
case BLE_GATTS_EVT_SYS_ATTR_MISSING:
{
err_code = sd_ble_gatts_sys_attr_set(p_gap_evt->conn_handle, NULL, 0, 0);
APP_ERROR_CHECK(err_code);
} break;
case BLE_GATTC_EVT_TIMEOUT: // Fallthrough.
case BLE_GATTS_EVT_TIMEOUT:
{
NRF_LOG_DEBUG("GATT timeout, disconnecting.\r\n");
err_code = sd_ble_gap_disconnect(m_conn_handle,
BLE_HCI_REMOTE_USER_TERMINATED_CONNECTION);
APP_ERROR_CHECK(err_code);
} break;
case BLE_EVT_USER_MEM_REQUEST:
{
err_code = sd_ble_user_mem_reply(p_ble_evt->evt.common_evt.conn_handle, NULL);
APP_ERROR_CHECK(err_code);
} break;
#if defined(S140)
case BLE_GAP_EVT_PHY_UPDATE:
{
ble_gap_evt_phy_update_t * const p_phy_evt = &p_ble_evt->evt.gap_evt.params.phy_update;
if (p_phy_evt->status == BLE_HCI_STATUS_CODE_LMP_ERROR_TRANSACTION_COLLISION)
{
// Ignore LL collisions.
NRF_LOG_DEBUG("LL transaction collision during PHY.\r\n");
break;
}
m_phy_updated = true;
NRF_LOG_INFO("PHY update %s. PHY set to %s.\r\n",
(p_phy_evt->status == BLE_HCI_STATUS_CODE_SUCCESS) ?
(uint32_t)"accepted" : (uint32_t)"rejected",
phy_str(p_phy_evt->tx_phy));
} break;
#endif
default:
// No implementation needed.
break;
}
}
/**@brief Function for dispatching a BLE stack event to all modules with a BLE stack event handler.
*
* @details This function is called from the BLE Stack event interrupt handler after a BLE stack
* event has been received.
*
* @param[in] p_ble_evt Bluetooth stack event.
*/
static void ble_evt_dispatch(ble_evt_t * p_ble_evt)
{
on_ble_evt(p_ble_evt);
ble_conn_params_on_ble_evt(p_ble_evt);
ble_db_discovery_on_ble_evt(&m_ble_db_discovery, p_ble_evt);
nrf_ble_gatt_on_ble_evt(&m_gatt, p_ble_evt);
nrf_ble_amts_on_ble_evt(&m_amts, p_ble_evt);
nrf_ble_amtc_on_ble_evt(&m_amtc, p_ble_evt);
}
/**@brief Function for handling events from the button handler module.
*
* @param[in] pin_no The pin that the event applies to.
* @param[in] button_action The button action (press/release).
*/
static void button_evt_handler(uint8_t pin_no, uint8_t button_action)
{
switch (pin_no)
{
case BOARD_TESTER_BUTTON:
{
NRF_LOG_INFO("This board will act as tester.\r\n");
m_board_role = BOARD_TESTER;
} break;
case BOARD_DUMMY_BUTTON:
{
NRF_LOG_INFO("This board will act as responder.\r\n");
m_board_role = BOARD_DUMMY;
} break;
default:
break;
}
}
/**@brief AMT Service Handler.
*/
static void amts_evt_handler(nrf_ble_amts_evt_t evt)
{
ret_code_t err_code;
switch (evt.evt_type)
{
case NRF_BLE_AMTS_EVT_NOTIF_ENABLED:
{
NRF_LOG_INFO("Notifications enabled.\r\n");
bsp_board_led_on(READY_LED);
m_notif_enabled = true;
if (m_board_role != BOARD_TESTER)
{
return;
}
if (m_gap_role == BLE_GAP_ROLE_PERIPH)
{
m_conn_interval_configured = false;
m_conn_param.min_conn_interval = m_test_params.conn_interval;
m_conn_param.max_conn_interval = m_test_params.conn_interval + 1;
err_code = ble_conn_params_change_conn_params(&m_conn_param);
if (err_code != NRF_SUCCESS)
{
NRF_LOG_ERROR("ble_conn_params_change_conn_params() failed: 0x%x.\r\n",
err_code);
}
}
if (m_gap_role == BLE_GAP_ROLE_CENTRAL)
{
m_conn_interval_configured = true;
m_conn_param.min_conn_interval = m_test_params.conn_interval;
m_conn_param.max_conn_interval = m_test_params.conn_interval;
err_code = sd_ble_gap_conn_param_update(m_conn_handle, &m_conn_param);
if (err_code != NRF_SUCCESS)
{
NRF_LOG_ERROR("sd_ble_gap_conn_param_update() failed: 0x%x.\r\n", err_code);
}
}
} break;
case NRF_BLE_AMTS_EVT_NOTIF_DISABLED:
{
NRF_LOG_INFO("Notifications disabled.\r\n");
bsp_board_led_off(READY_LED);
} break;
case NRF_BLE_AMTS_EVT_TRANSFER_1KB:
{
NRF_LOG_INFO("Sent %u KBytes\r\n", (evt.bytes_transfered_cnt / 1024));
bsp_board_led_invert(PROGRESS_LED);
} break;
case NRF_BLE_AMTS_EVT_TRANSFER_FINISHED:
{
counter_stop();
bsp_board_led_off(PROGRESS_LED);
bsp_board_led_on(DONE_LED);
uint32_t time_ms = counter_get();
uint32_t bit_count = (evt.bytes_transfered_cnt * 8);
float throughput_kbps = ((bit_count / (time_ms / 1000.f)) / 1000.f);
NRF_LOG_INFO("Done.\r\n\r\n");
NRF_LOG_INFO("=============================\r\n");
NRF_LOG_INFO("Time: %u.%.2u seconds elapsed.\r\n", (time_ms / 1000), (time_ms % 1000));
NRF_LOG_INFO("Throughput: " NRF_LOG_FLOAT_MARKER " Kbps.\r\n",
NRF_LOG_FLOAT(throughput_kbps));
NRF_LOG_INFO("=============================\r\n");
NRF_LOG_INFO("Sent %u bytes of ATT payload.\r\n", evt.bytes_transfered_cnt);
NRF_LOG_INFO("Retrieving amount of bytes received from peer...\r\n");
err_code = nrf_ble_amtc_rcb_read(&m_amtc);
if (err_code != NRF_SUCCESS)
{
NRF_LOG_ERROR("nrf_ble_amtc_rcb_read() failed: 0x%x.\r\n", err_code);
test_terminate();
}
} break;
}
}
/**@brief AMT Client Handler.
*/
static void amtc_evt_handler(nrf_ble_amtc_t * p_amt_c, nrf_ble_amtc_evt_t * p_evt)
{
ret_code_t err_code;
switch (p_evt->evt_type)
{
case NRF_BLE_AMT_C_EVT_DISCOVERY_COMPLETE:
{
NRF_LOG_INFO("AMT service discovered at peer.\r\n");
err_code = nrf_ble_amtc_handles_assign(p_amt_c,
p_evt->conn_handle,
&p_evt->params.peer_db);
APP_ERROR_CHECK(err_code);
// Enable notifications.
err_code = nrf_ble_amtc_notif_enable(p_amt_c);
APP_ERROR_CHECK(err_code);
} break;
case NRF_BLE_AMT_C_EVT_NOTIFICATION:
{
static uint32_t bytes_cnt = 0;
static uint32_t kbytes_cnt = 0;
if (p_evt->params.hvx.bytes_sent == 0)
{
bytes_cnt = 0;
kbytes_cnt = 0;
}
bytes_cnt += p_evt->params.hvx.notif_len;
if (bytes_cnt > 1024)
{
bsp_board_led_invert(PROGRESS_LED);
bytes_cnt -= 1024;
kbytes_cnt++;
NRF_LOG_INFO("Received %u kbytes\r\n", kbytes_cnt);
nrf_ble_amts_rbc_set(&m_amts, p_evt->params.hvx.bytes_rcvd);
}
if (p_evt->params.hvx.bytes_rcvd >= AMT_BYTE_TRANSFER_CNT)
{
bsp_board_led_off(PROGRESS_LED);
bytes_cnt = 0;
kbytes_cnt = 0;
NRF_LOG_INFO("Transfer complete, received %u bytes of ATT payload.\r\n",
p_evt->params.hvx.bytes_rcvd);
nrf_ble_amts_rbc_set(&m_amts, p_evt->params.hvx.bytes_rcvd);
}
} break;
case NRF_BLE_AMT_C_EVT_RBC_READ_RSP:
{
NRF_LOG_INFO("Peer received %u bytes of ATT payload.\r\n", (p_evt->params.rcv_bytes_cnt));
test_terminate();
} break;
default:
break;
}
}
/**@brief Function for handling Database Discovery events.
*
* @details This function is a callback function to handle events from the database discovery module.
* Depending on the UUIDs that are discovered, this function should forward the events
* to their respective service instances.
*
* @param[in] p_event Pointer to the database discovery event.
*/
static void db_disc_evt_handler(ble_db_discovery_evt_t * p_evt)
{
nrf_ble_amtc_on_db_disc_evt(&m_amtc, p_evt);
}
/**@brief Function for handling events from the GATT library. */
static void gatt_evt_handler(nrf_ble_gatt_t * p_gatt, nrf_ble_gatt_evt_t const * p_evt)
{
switch (p_evt->evt_id)
{
case NRF_BLE_GATT_EVT_ATT_MTU_UPDATED:
{
m_mtu_exchanged = true;
NRF_LOG_INFO("ATT MTU exchange completed. MTU set to %u bytes.\r\n",
p_evt->params.att_mtu_effective);
} break;
case NRF_BLE_GATT_EVT_DATA_LENGTH_UPDATED:
{
m_data_length_updated = true;
NRF_LOG_INFO("Data length updated to %u bytes.\r\n", p_evt->params.data_length);
} break;
}
nrf_ble_amts_on_gatt_evt(&m_amts, p_evt);
}
/**@brief Function for handling a Connection Parameters event.
*
* @param[in] p_evt event.
*/
static void conn_params_evt_handler(ble_conn_params_evt_t * p_evt)
{
if (p_evt->evt_type == BLE_CONN_PARAMS_EVT_SUCCEEDED)
{
m_conn_interval_configured = true;
}
}
/**@brief Function for handling a Connection Parameters error.
*
* @param[in] nrf_error Error code containing information about what went wrong.
*/
static void conn_params_error_handler(uint32_t nrf_error)
{
APP_ERROR_HANDLER(nrf_error);
}
/**@brief Function for setting up advertising data.
*/
static void advertising_data_set(void)
{
ble_advdata_t const adv_data =
{
.name_type = BLE_ADVDATA_FULL_NAME,
.flags = BLE_GAP_ADV_FLAGS_LE_ONLY_GENERAL_DISC_MODE,
.include_appearance = false,
};
ret_code_t err_code = ble_advdata_set(&adv_data, NULL);
APP_ERROR_CHECK(err_code);
}
/**@brief Function for starting advertising.
*/
static void advertising_start(void)
{
ble_gap_adv_params_t const adv_params =
{
.type = BLE_GAP_ADV_TYPE_ADV_IND,
.p_peer_addr = NULL,
.fp = BLE_GAP_ADV_FP_ANY,
.interval = ADV_INTERVAL,
.timeout = 0,
};
NRF_LOG_INFO("Starting advertising.\r\n");
bsp_board_led_on(SCAN_ADV_LED);
ret_code_t err_code = sd_ble_gap_adv_start(&adv_params, CONN_CFG_TAG);
APP_ERROR_CHECK(err_code);
}
/**@brief Function to start scanning.
*/
static void scan_start(void)
{
NRF_LOG_INFO("Starting scan.\r\n");
bsp_board_led_on(SCAN_ADV_LED);
ret_code_t err_code = sd_ble_gap_scan_start(&m_scan_param);
APP_ERROR_CHECK(err_code);
}
static void log_init(void)
{
ret_code_t err_code = NRF_LOG_INIT(NULL);
APP_ERROR_CHECK(err_code);
}
/**@brief Function for the LEDs initialization.
*
* @details Initializes all LEDs used by the application.
*/
static void leds_init(void)
{
bsp_board_leds_init();
}
/**@brief Function for the Timer initialization.
*
* @details Initializes the timer module. This creates and starts application timers.
*/
static void timer_init(void)
{
ret_code_t err_code = app_timer_init();
APP_ERROR_CHECK(err_code);
}
/**@brief Function for initializing the button library.
*/
static void buttons_init(void)
{
// The array must be static because a pointer to it will be saved in the button library.
static app_button_cfg_t buttons[] =
{
{BOARD_TESTER_BUTTON, false, BUTTON_PULL, button_evt_handler},
{BOARD_DUMMY_BUTTON, false, BUTTON_PULL, button_evt_handler}
};
ret_code_t err_code = app_button_init(buttons, ARRAY_SIZE(buttons), BUTTON_DETECTION_DELAY);
APP_ERROR_CHECK(err_code);
}
/**@brief Function for enabling button input.
*/
static void buttons_enable(void)
{
ret_code_t err_code = app_button_enable();
APP_ERROR_CHECK(err_code);
}
/**@brief Function for disabling button input.
*/
static void buttons_disable(void)
{
ret_code_t err_code = app_button_disable();
APP_ERROR_CHECK(err_code);
}
static void client_init(void)
{
ret_code_t err_code = ble_db_discovery_init(db_disc_evt_handler);
APP_ERROR_CHECK(err_code);
err_code = nrf_ble_amtc_init(&m_amtc, amtc_evt_handler);
APP_ERROR_CHECK(err_code);
}
static void server_init(void)
{
nrf_ble_amts_init(&m_amts, amts_evt_handler);
}
/**@brief Function for initializing the BLE stack.
*
* @details Initializes the SoftDevice and the BLE event interrupt.
*/
static void ble_stack_init(void)
{
ret_code_t err_code;
// Initialize the SoftDevice handler library.
nrf_clock_lf_cfg_t clock_lf_cfg = NRF_CLOCK_LFCLKSRC;
SOFTDEVICE_HANDLER_INIT(&clock_lf_cfg, NULL);
// Fetch the start address of the application RAM.
uint32_t ram_start = 0;
err_code = softdevice_app_ram_start_get(&ram_start);
APP_ERROR_CHECK(err_code);
// Overwrite some of the default configurations for the BLE stack.
ble_cfg_t ble_cfg;
// Configure the maximum number of connections.
memset(&ble_cfg, 0x00, sizeof(ble_cfg));
ble_cfg.gap_cfg.role_count_cfg.periph_role_count = 1;
ble_cfg.gap_cfg.role_count_cfg.central_role_count = 1;
ble_cfg.gap_cfg.role_count_cfg.central_sec_count = 1;
err_code = sd_ble_cfg_set(BLE_GAP_CFG_ROLE_COUNT, &ble_cfg, ram_start);
APP_ERROR_CHECK(err_code);
// Configure the maximum ATT MTU.
memset(&ble_cfg, 0x00, sizeof(ble_cfg));
ble_cfg.conn_cfg.conn_cfg_tag = CONN_CFG_TAG;
ble_cfg.conn_cfg.params.gatt_conn_cfg.att_mtu = NRF_BLE_GATT_MAX_MTU_SIZE;
err_code = sd_ble_cfg_set(BLE_CONN_CFG_GATT, &ble_cfg, ram_start);
APP_ERROR_CHECK(err_code);
// Configure the maximum event length.
memset(&ble_cfg, 0x00, sizeof(ble_cfg));
ble_cfg.conn_cfg.conn_cfg_tag = CONN_CFG_TAG;
ble_cfg.conn_cfg.params.gap_conn_cfg.event_length = 320;
ble_cfg.conn_cfg.params.gap_conn_cfg.conn_count = BLE_GAP_CONN_COUNT_DEFAULT;
err_code = sd_ble_cfg_set(BLE_CONN_CFG_GAP, &ble_cfg, ram_start);
APP_ERROR_CHECK(err_code);
// Configure the number of custom UUIDs.
memset(&ble_cfg, 0x00, sizeof(ble_cfg));
ble_cfg.common_cfg.vs_uuid_cfg.vs_uuid_count = 1;
err_code = sd_ble_cfg_set(BLE_COMMON_CFG_VS_UUID, &ble_cfg, ram_start);
APP_ERROR_CHECK(err_code);
// Enable BLE stack.
err_code = softdevice_enable(&ram_start);
APP_ERROR_CHECK(err_code);
// Register a BLE event handler with the SoftDevice handler library.
err_code = softdevice_ble_evt_handler_set(ble_evt_dispatch);
APP_ERROR_CHECK(err_code);
}
/**@brief Function for initializing GAP parameters.
*
* @details This function sets up all the necessary GAP (Generic Access Profile) parameters of the
* device including the device name and the preferred connection parameters.
*/
static void gap_params_init(void)
{
ret_code_t err_code;
ble_gap_conn_sec_mode_t sec_mode;
BLE_GAP_CONN_SEC_MODE_SET_OPEN(&sec_mode);
err_code = sd_ble_gap_device_name_set(&sec_mode,
(uint8_t const *)DEVICE_NAME,
strlen(DEVICE_NAME));
APP_ERROR_CHECK(err_code);
err_code = sd_ble_gap_ppcp_set(&m_conn_param);
APP_ERROR_CHECK(err_code);
}
/**@brief Function for initializing the GATT library. */
static void gatt_init(void)
{
ret_code_t err_code = nrf_ble_gatt_init(&m_gatt, gatt_evt_handler);
APP_ERROR_CHECK(err_code);
}
static void wait_for_event(void)
{
(void) sd_app_evt_wait();
}
/**@brief Function for initializing the Connection Parameters module.
*/
static void conn_params_init(void)
{
ble_conn_params_init_t const connection_params_init =
{
.p_conn_params = NULL,
.first_conn_params_update_delay = FIRST_CONN_PARAMS_UPDATE_DELAY,
.next_conn_params_update_delay = NEXT_CONN_PARAMS_UPDATE_DELAY,
.max_conn_params_update_count = MAX_CONN_PARAMS_UPDATE_COUNT,
.disconnect_on_fail = true,
.evt_handler = conn_params_evt_handler,
.error_handler = conn_params_error_handler,
};
ret_code_t err_code = ble_conn_params_init(&connection_params_init);
APP_ERROR_CHECK(err_code);
}
#ifdef S140
static void preferred_phy_set(uint8_t phy)
{
ble_opt_t opts;
memset(&opts, 0x00, sizeof(ble_opt_t));
opts.gap_opt.preferred_phys.tx_phys = phy;
opts.gap_opt.preferred_phys.rx_phys = phy;
ret_code_t err_code = sd_ble_opt_set(BLE_GAP_OPT_PREFERRED_PHYS_SET, &opts);
APP_ERROR_CHECK(err_code);
NRF_LOG_DEBUG("Setting preferred phy (rxtx) to %u: 0x%x\r\n", phy, err_code);
}
#endif
static void gatt_mtu_set(uint16_t att_mtu)
{
ret_code_t err_code;
err_code = nrf_ble_gatt_att_mtu_periph_set(&m_gatt, att_mtu);
APP_ERROR_CHECK(err_code);
err_code = nrf_ble_gatt_att_mtu_central_set(&m_gatt, att_mtu);
APP_ERROR_CHECK(err_code);
}
static void conn_evt_len_ext_set(bool status)
{
ret_code_t err_code;
ble_opt_t opt;
memset(&opt, 0x00, sizeof(opt));
opt.common_opt.conn_evt_ext.enable = status ? 1 : 0;
err_code = sd_ble_opt_set(BLE_COMMON_OPT_CONN_EVT_EXT, &opt);
APP_ERROR_CHECK(err_code);
NRF_LOG_DEBUG("Setting connection event length extension to %u: 0x%x\r\n", status, err_code);
}
static void data_len_ext_set(bool status)
{
uint8_t data_length = status ? (247 + LL_HEADER_LEN) : (23 + LL_HEADER_LEN);
(void) nrf_ble_gatt_data_length_set(&m_gatt, BLE_CONN_HANDLE_INVALID, data_length);
}
#if defined(S140)
static void preferred_phy_select(void)
{
NRF_LOG_INFO("Select preferred PHY:\r\n");
NRF_LOG_INFO(" 1) 1 Mbps.\r\n");
NRF_LOG_INFO(" 2) 2 Mbps.\r\n");
NRF_LOG_INFO(" 3) Coded.\r\n");
NRF_LOG_FLUSH();
switch (NRF_LOG_GETCHAR())
{
default:
case ONE:
m_test_params.rxtx_phy = BLE_GAP_PHY_1MBPS;
break;
case TWO:
m_test_params.rxtx_phy = BLE_GAP_PHY_2MBPS;
break;
case THREE:
m_test_params.rxtx_phy = BLE_GAP_PHY_CODED;
break;
}
preferred_phy_set(m_test_params.rxtx_phy);
NRF_LOG_INFO("Preferred PHY set to %s.\r\n", phy_str(m_test_params.rxtx_phy));
NRF_LOG_FLUSH();
}
#endif
static void att_mtu_select(void)
{
NRF_LOG_INFO("Select an ATT MTU size:\r\n");
NRF_LOG_INFO(" 1) 23 bytes.\r\n");
NRF_LOG_INFO(" 2) 158 bytes.\r\n");
NRF_LOG_INFO(" 3) 247 bytes.\r\n");
NRF_LOG_FLUSH();
switch (NRF_LOG_GETCHAR())
{
default:
case ONE:
m_test_params.att_mtu = 23;
break;
case TWO:
m_test_params.att_mtu = 158;
break;
case THREE:
m_test_params.att_mtu = 247;
break;
}
gatt_mtu_set(m_test_params.att_mtu);
NRF_LOG_INFO("ATT MTU set to %u bytes.\r\n", m_test_params.att_mtu);
NRF_LOG_FLUSH();
}
static void conn_interval_select(void)
{
NRF_LOG_INFO("Select a connection interval:\r\n");
NRF_LOG_INFO(" 1) 7.5 ms\r\n");
NRF_LOG_INFO(" 2) 50 ms\r\n");
NRF_LOG_INFO(" 3) 400 ms\r\n");
NRF_LOG_FLUSH();
switch (NRF_LOG_GETCHAR())
{
default:
case ONE:
m_test_params.conn_interval = (uint16_t)(MSEC_TO_UNITS(7.5, UNIT_1_25_MS));
NRF_LOG_INFO("Connection interval set to 7.5 ms.\r\n");
break;
case TWO:
m_test_params.conn_interval = (uint16_t)(MSEC_TO_UNITS(50, UNIT_1_25_MS));
NRF_LOG_INFO("Connection interval set to 50 ms.\r\n");
break;
case THREE:
m_test_params.conn_interval = (uint16_t)(MSEC_TO_UNITS(400, UNIT_1_25_MS));
NRF_LOG_INFO("Connection interval set to 400 ms.\r\n");
break;
}
NRF_LOG_FLUSH();
}
static void data_len_ext_select(void)
{
NRF_LOG_INFO("Turn on Data Length Extension? (y/n)\r\n");
NRF_LOG_FLUSH();
char answer = NRF_LOG_GETCHAR();
m_test_params.data_len_ext_enabled = (answer == YES) ? 1 : 0;
data_len_ext_set(m_test_params.data_len_ext_enabled);
NRF_LOG_INFO("Data Length Extension is %s\r\n", (answer == YES) ?
(uint32_t) "ON" :
(uint32_t) "OFF");
NRF_LOG_FLUSH();
}
static void test_param_adjust(void)
{
bool done = false;
while (!done)
{
NRF_LOG_RAW_INFO("\r\n");
NRF_LOG_INFO("Adjust test parameters:\r\n");
NRF_LOG_INFO(" 1) Select ATT MTU size.\r\n");
NRF_LOG_INFO(" 2) Select connection interval.\r\n");
NRF_LOG_INFO(" 3) Turn on/off Data length extension (DLE).\r\n");
#if defined(S140)
NRF_LOG_INFO(" 4) Select preferred PHY.\r\n")
#endif
NRF_LOG_RAW_INFO("\r\n");
NRF_LOG_INFO("Press ENTER when finished.\r\n");
NRF_LOG_RAW_INFO("\r\n");
NRF_LOG_FLUSH();
switch (NRF_LOG_GETCHAR())
{
case ONE:
att_mtu_select();
break;
case TWO:
conn_interval_select();
break;
case THREE:
data_len_ext_select();
break;
#if defined(S140)
case FOUR:
preferred_phy_select();
break;
#endif
default:
case ENTER:
done = true;
break;
}
}
}
static void test_params_print(void)
{
NRF_LOG_RAW_INFO("\r\n");
NRF_LOG_INFO("Current test configuration:\r\n");
NRF_LOG_INFO("===============================\r\n");
NRF_LOG_INFO("ATT MTU size: %u\r\n", m_test_params.att_mtu);
NRF_LOG_INFO("Conn. interval: %u units (1.25 ms per unit).\r\n", m_test_params.conn_interval);
NRF_LOG_INFO("Data length extension (DLE): %s\r\n", m_test_params.data_len_ext_enabled ?
(uint32_t)"ON" :
(uint32_t)"OFF");
NRF_LOG_DEBUG("Conn. event length ext.: %s\r\n", m_test_params.conn_evt_len_ext_enabled ?
(uint32_t)"ON" :
(uint32_t)"OFF");
#if defined(S140)
NRF_LOG_INFO("Preferredy PHY: %s\r\n", phy_str(m_test_params.rxtx_phy));
#endif
NRF_LOG_INFO("===============================\r\n");
NRF_LOG_RAW_INFO("\r\n");
NRF_LOG_FLUSH();
}
static void test_begin(void)
{
NRF_LOG_INFO("Preparing the test.\r\n");
NRF_LOG_FLUSH();
switch (m_gap_role)
{
default:
// If no connection was established, the role won't be either.
// In this case, start both advertising and scanning.
advertising_start();
scan_start();
break;
case BLE_GAP_ROLE_PERIPH:
advertising_start();
break;
case BLE_GAP_ROLE_CENTRAL:
scan_start();
break;
}
}
static void test_run(void)
{
NRF_LOG_RAW_INFO("\r\n");
NRF_LOG_INFO("Test is ready. Press any key to run.\r\n");
NRF_LOG_FLUSH();
(void) NRF_LOG_GETCHAR();
counter_start();
nrf_ble_amts_notif_spam(&m_amts);
}
static void test_terminate(void)
{
m_run_test = false;
m_notif_enabled = false;
m_mtu_exchanged = false;
m_data_length_updated = false;
#if defined(S140)
m_phy_updated = false;
#endif
m_conn_interval_configured = false;
if (m_conn_handle != BLE_CONN_HANDLE_INVALID)
{
NRF_LOG_INFO("Disconnecting...\r\n");
ret_code_t err_code;
err_code = sd_ble_gap_disconnect(m_conn_handle, BLE_HCI_REMOTE_USER_TERMINATED_CONNECTION);
if (err_code != NRF_SUCCESS)
{
NRF_LOG_ERROR("sd_ble_gap_disconnect() failed: 0x%0x.\r\n", err_code);
}
}
else
{
if (m_board_role == BOARD_TESTER)
{
m_print_menu = true;
}
if (m_board_role == BOARD_DUMMY)
{
if (m_gap_role == BLE_GAP_ROLE_PERIPH)
{
advertising_start();
}
else
{
scan_start();
}
}
}
}
static void menu_print(void)
{
bool begin_test = false;
while (!begin_test)
{
test_params_print();
NRF_LOG_INFO("Throughput example:\r\n");
NRF_LOG_INFO(" 1) Run test.\r\n");
NRF_LOG_INFO(" 2) Adjust test parameters.\r\n");
NRF_LOG_FLUSH();
switch (NRF_LOG_GETCHAR())
{
case ONE:
default:
begin_test = true;
test_begin();
break;
case TWO:
test_param_adjust();
break;
}
}
m_print_menu = false;
}
static bool is_test_ready()
{
return ( (m_board_role == BOARD_TESTER)
&& m_conn_interval_configured
&& m_notif_enabled
&& m_mtu_exchanged
&& m_data_length_updated
#if defined(S140)
&& m_phy_updated
#endif
&& !m_run_test);
}
static void board_role_select(void)
{
buttons_enable();
while (m_board_role == NOT_SELECTED)
{
wait_for_event();
}
buttons_disable();
}
int main(void)
{
log_init();
leds_init();
timer_init();
counter_init();
buttons_init();
ble_stack_init();
gap_params_init();
conn_params_init();
gatt_init();
advertising_data_set();
server_init();
client_init();
gatt_mtu_set(m_test_params.att_mtu);
data_len_ext_set(m_test_params.data_len_ext_enabled);
conn_evt_len_ext_set(m_test_params.conn_evt_len_ext_enabled);
#if defined(S140)
preferred_phy_set(m_test_params.rxtx_phy);
#endif
NRF_LOG_INFO("ATT MTU example started.\r\n");
NRF_LOG_INFO("Press button 3 on the board connected to the PC.\r\n");
NRF_LOG_INFO("Press button 4 on other board.\r\n");
NRF_LOG_FLUSH();
board_role_select();
if (m_board_role == BOARD_TESTER)
{
m_print_menu = true;
}
if (m_board_role == BOARD_DUMMY)
{
advertising_start();
scan_start();
}
// Enter main loop.
NRF_LOG_DEBUG("Entering main loop.\r\n");
for (;;)
{
if (m_print_menu)
{
menu_print();
}
if (is_test_ready())
{
m_run_test = true;
test_run();
}
if (!NRF_LOG_PROCESS())
{
wait_for_event();
}
}
}
/**
* @}
*/
|
opplatek/deSALT | src/deBGA-master/seed_ali_core.c |
#include <time.h>
#include <ctype.h>
#include <inttypes.h>
#include <omp.h>
#include <math.h>
//#include "global.h"
#include "binarys_qsort.h"
#include "LandauVishkin.h"
#include "seed_ali_p.h"
#include "bit_operation.h"
#include "ksw.h"
#ifdef PTHREAD_USE
#include <pthread.h>
#ifdef R_W_LOCK
static void *worker(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
int _read_seq;
while (1)
{
pthread_rwlock_wrlock(&rwlock);
_read_seq = read_seq++;
pthread_rwlock_unlock(&rwlock);
if (_read_seq < d->seqn)
{
seed_ali_core(_read_seq, d->tid);
}
else break;
}
return 0;
}
static void *worker_single_end(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
int _read_seq;
while (1)
{
pthread_rwlock_wrlock(&rwlock);
_read_seq = read_seq++;
pthread_rwlock_unlock(&rwlock);
if (_read_seq < d->seqn)
{
seed_ali_core_single_end(_read_seq, d->tid);
}
else break;
}
return 0;
}
#else
static void *worker(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
seed_ali_core(d->seqn, d->tid);
return 0;
}
static void *worker_single_end(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
seed_ali_core_single_end(d->seqn, d->tid);
return 0;
}
#endif
#endif
int seed_ali()
{
fprintf(stderr, "pair end reads mapping\n\n");
double t = 0.00;
clock_t start = 0, end = 0;
uint8_t readlen_name = 200;
uint16_t v_cnt_i = 0;
//uint16_t read_bit_char = 0;
uint32_t r_i = 0;
uint32_t seqi = 0;
uint32_t seqii = 0;
uint32_t read_in = 0X10000;
int32_t l, m, k1;//maybe changed here
int64_t kr1 = 1;
int64_t kr2 = 1;
char h_chars[6];
#ifdef PAIR_RANDOM_SEED
uint32_t r_dup_i = 0;
uint32_t pos_r_ir = 0;
int pos_r_nr = 0;
#endif
start = clock();
load_index_file();
end = clock();
t = (double)(end - start) / CLOCKS_PER_SEC;
fp1 = gzopen(read_fastq1, "r");
seq1 = kseq_init(fp1);
fp2 = gzopen(read_fastq2, "r");
seq2 = kseq_init(fp2);
if((fp1 == NULL) || (fp2 == NULL))
{
fprintf(stderr, "wrong input file route or name: %s %s\n", read_fastq1, read_fastq2);
exit(1);
}
if(flag_std == 0)
{
fp_sam = fopen(sam_result, "w");
if(fp_sam == NULL)
{
fprintf(stderr, "wrong output file route or name: %s\n", sam_result);
exit(1);
}
}
seed_l_max = seed_step * cir_fix_n;
insert_dis = (upper_ins + floor_ins) >> 1;
devi = (upper_ins - floor_ins) >> 1;
pair_ran_intvp = seed_l_max;
#ifdef SEED_FILTER_POS
seed_filter_pos_num = seed_filter_pos_numn >> 2;
#endif
//fprintf(stderr, "number of threads: %u\nkmer size: %u\ninsert size: %u\nstandard varaiance: %"PRId64"\nseed interval: %u\nthe max read length: %u\nmax lv error rate: %.2f\nmax pair error rate: %.2f\nthe minimum seed interval: %u\nthe number of seed circulation: %u\nlv rate on anchor: %.2f\nthe max rate of mismatch alignment on anchor: %.2f\n", thread_n, k_t, insert_dis, (devi / 3), pair_ran_intvp, readlen_max, lv_rate, max_pair_score_r, seed_step, cir_fix_n, lv_rate_anchor, mis_match_r_single);
fprintf(stderr, "number of threads: %u\nkmer size: %u\nseed interval: %u\nthe max read length: %u\nmax lv error rate: %.2f\nmax pair error rate: %.2f\nthe minimum seed interval: %u\nthe number of seed circulation: %u\nlv rate on anchor: %.2f\nthe max rate of mismatch alignment on anchor: %.2f\n", thread_n, k_t, pair_ran_intvp, readlen_max, lv_rate, max_pair_score_r, seed_step, cir_fix_n, lv_rate_anchor, mis_match_r_single);
fprintf(stderr, "local alignment score match: %d mismatch: %d gap open: %d gap extension: %d\n", mat_score, mis_score, gapo_score, gape_score);
fprintf(stderr, "%lf seconds is used for loading index\n", t);
if(local_ksw) fprintf(stderr, "use local sw alignment\n");
if(last_circle_rate) fprintf(stderr, "use last circle end-to-end alignment and the max rate of alignment score is %.2f\n", last_circle_rate);
if(!mgn_flag) fprintf(stderr, "use the mode of multi-genomes\n");
#ifdef LV_MP
fprintf(stderr, "cal mapping quality on LV\n");
#endif
#ifdef QUAL_ANCHOR
fprintf(stderr, "use quality in anchor\n");
#endif
if(flag_std)
fprintf(stderr, "output alignments by stdout\n");
k_r = k_t - k;
re_b = 32 - k_t;
re_bt = (re_b << 1);
re_2bt = 64 - k_t;
//should allocate at beginning
seed_num = ((readlen_max - k_t) / seed_l_l) + 1;
new_seed_cnt = seed_num * pos_n_max;
uint16_t cigar_max_n = MAX_LV_CIGARCOM;
#ifdef STA_SEED
fp_read = fopen(file_read, "w");
fp_seed = fopen(file_seed, "w");
#endif
//allocation
start = clock();
#ifdef PTHREAD_USE
#ifdef ANCHOR_HASH_ALI
anchor_hash = (uint16_t*** )calloc(thread_n, sizeof(uint16_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_hash[r_i] = (uint16_t** )calloc(4, sizeof(uint16_t* ));
for(m = 0; m < 4; m++) anchor_hash[r_i][m] = (uint16_t* )calloc(1 << 16, 2);
}
anchor_array = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_array[r_i] = (uint8_t** )calloc(4, sizeof(uint8_t* ));
for(m = 0; m < 4; m++) anchor_array[r_i][m] = (uint8_t* )calloc(readlen_max - k_anchor + 1, 1);
}
anchor_point = (uint16_t*** )calloc(thread_n, sizeof(uint16_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_point[r_i] = (uint16_t** )calloc(4, sizeof(uint16_t* ));
for(m = 0; m < 4; m++) anchor_point[r_i][m] = (uint16_t* )calloc(readlen_max - k_anchor + 1, 2);
}
anchor_pos = (uint16_t*** )calloc(thread_n, sizeof(uint16_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_pos[r_i] = (uint16_t** )calloc(4, sizeof(uint16_t* ));
for(m = 0; m < 4; m++) anchor_pos[r_i][m] = (uint16_t* )calloc(readlen_max - k_anchor + 1, 2);
}
rh = (read_h** )calloc(thread_n, sizeof(read_h* ));
for(r_i = 0; r_i < thread_n; r_i++)
rh[r_i] = (read_h* )calloc(readlen_max - k_anchor + 1, sizeof(read_h));
anchor_seed_buffer = (anchor_seed** )calloc(thread_n, sizeof(anchor_seed* ));
for(r_i = 0; r_i < thread_n; r_i++)
anchor_seed_buffer[r_i] = (anchor_seed* )calloc((readlen_max - k_anchor + 1) * insert_dis, sizeof(anchor_seed));
#endif
g_low = (int64_t* )calloc(thread_n, 8);
r_low = (int64_t* )calloc(thread_n, 8);
seedm = (seed_m** )calloc(thread_n, sizeof(seed_m* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedm[r_i] = (seed_m* )calloc(seed_num, sizeof(seed_m));
seedu = (seed_m** )calloc(thread_n, sizeof(seed_m* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedu[r_i] = (seed_m* )calloc(seed_num, sizeof(seed_m));
seedsets = (seed_sets** )calloc(thread_n, sizeof(seed_sets* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedsets[r_i] = (seed_sets* )calloc(new_seed_cnt, sizeof(seed_sets));
seed_set_off = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_off[r_i] = (uint32_t* )calloc(new_seed_cnt, sizeof(uint32_t ));
#ifdef UNPIPATH_OFF_K20
seed_set_pos[0][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][0][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
seed_set_pos[0][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][1][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
seed_set_pos[1][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][0][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
seed_set_pos[1][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][1][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
#else
seed_set_pos[0][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][0][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
seed_set_pos[0][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][1][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
seed_set_pos[1][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][0][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
seed_set_pos[1][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][1][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
#endif
seedpa1[0] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa1[0][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
seedpa1[1] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa1[1][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
seedpa2[0] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa2[0][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
seedpa2[1] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa2[1][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
fprintf(stderr, "Load seed reduction allocation\n");
#ifdef ALTER_DEBUG
seed_length_arr = (seed_length_array** )calloc(thread_n, sizeof(seed_length_array* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_length_arr[r_i] = (seed_length_array* )calloc(cus_max_output_ali, sizeof(seed_length_array));
rep_go = (uint8_t* )calloc(thread_n, 1);
#endif
#ifdef UNPIPATH_OFF_K20
#ifdef REDUCE_ANCHOR
poses1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses1[r_i] = (uint64_t* )calloc(cus_max_output_ali << 1, 8);
poses2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses2[r_i] = (uint64_t* )calloc(cus_max_output_ali << 1, 8);
#endif
op_vector_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos1[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
op_vector_pos2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos2[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
ops_vector_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos1[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
ops_vector_pos2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos2[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
#else
#ifdef REDUCE_ANCHOR
poses1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses1[r_i] = (uint32_t* )calloc(cus_max_output_ali << 1, 4);
poses2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses2[r_i] = (uint32_t* )calloc(cus_max_output_ali << 1, 4);
#endif
op_vector_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos1[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
op_vector_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos2[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
ops_vector_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos1[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
ops_vector_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos2[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
#endif
#ifdef REDUCE_ANCHOR
ls1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ls1[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
rs1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
rs1[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
ls2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ls2[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
rs2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
rs2[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
#endif
op_dm_l1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_l1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_r1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_r1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_l2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_l2[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_r2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_r2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_l1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_l1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_r1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_r1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_l2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_l2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_r2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_r2[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_ex1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_ex1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_ex2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_ex2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_ex1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_ex1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_ex2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_ex2[r_i] = (int* )calloc(cus_max_output_ali, 4);
//for S
#ifdef QUALS_CHECK
op_err = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_err[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ops_err = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_err[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
#endif
op_vector_seq1 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
op_vector_seq1[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((op_vector_seq1[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
op_vector_seq2 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
op_vector_seq2[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((op_vector_seq2[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
ops_vector_seq1 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
ops_vector_seq1[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((ops_vector_seq1[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
ops_vector_seq2 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
ops_vector_seq2[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((ops_vector_seq2[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
fprintf(stderr, "Load alignment allocation\n");
#ifdef ALT_ALL
chr_res = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
chr_res[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
sam_pos1s = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
if((sam_pos1s[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(uint32_t ))) == NULL)
exit(1);
sam_pos2s = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
if((sam_pos2s[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(uint32_t ))) == NULL)
exit(1);
cigar_p1s = (char*** )calloc(thread_n, sizeof(char** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
cigar_p1s[r_i] = (char** )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(char* ));
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if((cigar_p1s[r_i][m] = (char* )calloc(cigar_max_n, 1)) == NULL)
exit(1);
}
cigar_p2s = (char*** )calloc(thread_n, sizeof(char** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
cigar_p2s[r_i] = (char** )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(char* ));
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if((cigar_p2s[r_i][m] = (char* )calloc(cigar_max_n, 1)) == NULL)
exit(1);
}
xa_d1s = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
xa_d1s[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
xa_d2s = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
xa_d2s[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
lv_re1s = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
lv_re1s[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(int));
lv_re2s = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
lv_re2s[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(int));
#endif
fprintf(stderr, "Load output allocation\n");
#ifdef REDUCE_ANCHOR
rcs1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
rcs1[r_i] = (uint8_t* )calloc(cus_max_output_ali << 1, 1);
rcs2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
rcs2[r_i] = (uint8_t* )calloc(cus_max_output_ali << 1, 1);
#endif
op_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_rc[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ops_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_rc[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ref_seq_tmp1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ref_seq_tmp1[r_i] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8);
ref_seq_tmp2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ref_seq_tmp2[r_i] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8);
#ifdef UNPIPATH_OFF_K20
mat_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos1[r_i] = (uint64_t* )calloc(CUS_SEED_SET, 8);
mat_pos2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos2[r_i] = (uint64_t* )calloc(CUS_SEED_SET, 8);
#else
mat_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos1[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
mat_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos2[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
#endif
mat_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_rc[r_i] = (uint8_t* )calloc(CUS_SEED_SET, 1);
seed_no1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_no1[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
seed_no2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_no2[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
fprintf(stderr, "Load alignment more allocation\n");
#ifdef PAIR_RANDOM
#ifdef UNPIPATH_OFF_K20
seedpos[0][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][0][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seedpos[0][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][1][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seedpos[1][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][0][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seedpos[1][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][1][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seed_single_pos[0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[0][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seed_single_pos[1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[1][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seed_k_pos = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++) //2000
{
seed_k_pos[r_i] = (uint64_t** )calloc(readlen_max / pair_ran_intvp, sizeof(uint64_t* ));
for(m = 0; m < readlen_max / pair_ran_intvp; m++)
if((seed_k_pos[r_i][m] = (uint64_t* )calloc(RANDOM_RANGE, 8)) == NULL)
exit(1);
}
seedposk = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedposk[r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
#else
seedpos[0][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][0][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seedpos[0][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][1][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seedpos[1][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][0][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seedpos[1][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][1][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_pos[0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[0][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_pos[1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[1][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_k_pos = (uint32_t*** )calloc(thread_n, sizeof(uint32_t** ));
for(r_i = 0; r_i < thread_n; r_i++) //2000
{
seed_k_pos[r_i] = (uint32_t** )calloc(readlen_max / pair_ran_intvp, sizeof(uint32_t* ));
for(m = 0; m < readlen_max / pair_ran_intvp; m++)
if((seed_k_pos[r_i][m] = (uint32_t* )calloc(RANDOM_RANGE, 4)) == NULL)
exit(1);
}
seedposk = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedposk[r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
#endif
seed_posf[0] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_posf[0][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seed_posf[1] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_posf[1][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seed_single_ld[0] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_ld[0][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_ld[1] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_ld[1][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_rd[0] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_rd[0][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_rd[1] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_rd[1][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_dm[0] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_dm[0][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_dm[1] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_dm[1][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
if((seed_single_refs[0] = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ))) == NULL)
exit(1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if((seed_single_refs[0][r_i] = (uint64_t** )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, sizeof(uint64_t* ))) == NULL)
exit(1);
for(m = 0; m < (readlen_max / pair_ran_intvp) * RANDOM_RANGE; m++)
{
if((seed_single_refs[0][r_i][m] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8)) == NULL)
exit(1);
}
}
if((seed_single_refs[1] = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ))) == NULL)
exit(1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if((seed_single_refs[1][r_i] = (uint64_t** )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, sizeof(uint64_t* ))) == NULL)
exit(1);
for(m = 0; m < (readlen_max / pair_ran_intvp) * RANDOM_RANGE; m++)
{
if((seed_single_refs[1][r_i][m] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8)) == NULL)
exit(1);
}
}
#ifdef PR_SINGLE
seedpos_mis[0][0] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[0][0][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seedpos_mis[0][1] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[0][1][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seedpos_mis[1][0] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[1][0][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seedpos_mis[1][1] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[1][1][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
pr_chr_res1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_chr_res1[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
pr_sam_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_sam_pos1[r_i] = (uint32_t* )calloc(pr_single_outputn, 4);
pr_xa_d1 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_xa_d1[r_i] = (char* )calloc(pr_single_outputn, 1);
pr_lv_re1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_lv_re1[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
pr_chr_res2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_chr_res2[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
pr_sam_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_sam_pos2[r_i] = (uint32_t* )calloc(pr_single_outputn, 4);
pr_xa_d2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_xa_d2[r_i] = (char* )calloc(pr_single_outputn, 1);
pr_lv_re2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_lv_re2[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
#endif
fprintf(stderr, "Load pair random allocation\n");
#ifdef PAIR_RANDOM_SEED
seed_r_dup = (uint32_t* )calloc(RANDOM_RANGE, 4);
srand((unsigned)time(0));
pos_r_nr = RANDOM_RANGE;
r_dup_i = 0;
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE_MAX; pos_r_ir++)
if((rand() % (RANDOM_RANGE_MAX - pos_r_ir)) < pos_r_nr)
{
seed_r_dup[r_dup_i++] = pos_r_ir;
pos_r_nr--;
}
random_buffer = (uint32_t* )malloc((RAN_CIR) << 2);
for(pos_r_ir = 0; pos_r_ir < RAN_CIR; pos_r_ir++)
random_buffer[pos_r_ir] = (uint32_t )rand();
#endif
#endif
#ifdef READN_RANDOM_SEED
random_buffer_readn = (uint32_t* )calloc(RANDOM_RANGE_READN, 4);
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE_READN; pos_r_ir++)
random_buffer_readn[pos_r_ir] = (uint32_t )rand();
#endif
//thread gloabl value
rc_cov_f = (uint8_t* )calloc(thread_n, 1);
cov_a_n = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
cov_a_n[r_i] = (uint8_t* )calloc(2,1);
cov_a_n_s = (uint8_t* )calloc(thread_n, 1);
s_uid_f = (uint8_t* )calloc(thread_n, 1);
min_mis = (uint8_t* )calloc(thread_n, 1);
de_m_p = (uint8_t* )calloc(thread_n, 1);
de_m_p_o = (uint8_t* )calloc(thread_n, 1);
seed_l = (int16_t* )calloc(thread_n, 2);//cannot be 0
max_mismatch1 = (uint16_t* )calloc(thread_n, 2);
max_mismatch2 = (uint16_t* )calloc(thread_n, 2);
max_mismatch1_single = (uint16_t* )calloc(thread_n, 2);
max_mismatch2_single = (uint16_t* )calloc(thread_n, 2);
#ifdef PR_SINGLE
pr_o_f = (uint8_t* )calloc(thread_n, 1);
seed_re_r = (uint8_t* )calloc(thread_n, 1);
#endif
end_dis1 = (uint16_t* )calloc(thread_n, 2);
end_dis2 = (uint16_t* )calloc(thread_n, 2);
mat_posi = (uint32_t* )calloc(thread_n, 4);
#ifdef PAIR_SEED_LENGTH_FILT
max_lengtht = (uint32_t* )calloc(thread_n, 4);
#endif
#ifdef REDUCE_ANCHOR
orders1 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
orders1[r_i] = (uint16_t* )calloc(cus_max_output_ali << 1, 2);
orders2 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
orders2[r_i] = (uint16_t* )calloc(cus_max_output_ali << 1, 2);
dms1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
dms1[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
dms2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
dms2[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
#endif
dm_op = (int* )calloc(thread_n, 4);
dm_ops = (int* )calloc(thread_n, 4);
low_mask1 = (uint64_t* )calloc(thread_n, 8);
low_mask2 = (uint64_t* )calloc(thread_n, 8);
pos_add = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pos_add[r_i] = (uint8_t* )calloc(pos_n_max, 1);
cigar_m1 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
cigar_m1[r_i] = (char* )calloc(CIGARMN, 1);
cigar_m2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
cigar_m2[r_i] = (char* )calloc(CIGARMN, 1);
ali_ref_seq = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
ali_ref_seq[r_i] = (char* )calloc(readlen_max + 64, 1);
read_char = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
read_char[r_i] = (char* )calloc(readlen_max + 32, 1);
pos_ren[0][0] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[0][1] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[1][0] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[1][1] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
sub_mask1 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
sub_mask1[r_i] = (uint16_t* )calloc(33, 2);
sub_mask2 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
sub_mask2[r_i] = (uint16_t* )calloc(33, 2);
seedpos_misn[0][0] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
seedpos_misn[0][1] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
seedpos_misn[1][0] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
seedpos_misn[1][1] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
ex_d_mask1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ex_d_mask1[r_i] = (uint64_t* )calloc(33, 8);
ex_d_mask2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ex_d_mask2[r_i] = (uint64_t* )calloc(33, 8);
#ifdef PAIR_RANDOM
#ifdef UNPIPATH_OFF_K20
b = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
b[r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) + 1, 8);
#else
b = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
b[r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) + 1, 4);
#endif
ls = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ls[r_i] = (uint32_t* )calloc(readlen_max / pair_ran_intvp, 4);
read_bit_pr = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
read_bit_pr[r_i] = (uint64_t** )calloc(4, sizeof(uint64_t* ));
read_val_pr = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
read_val_pr[r_i] = (uint8_t** )calloc(4, sizeof(uint8_t* ));
kcol = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
kcol[r_i] = (uint32_t* )calloc(readlen_max / pair_ran_intvp, 4);
seed_posn[0] = (uint32_t* )calloc(thread_n, 4);
seed_posn[1] = (uint32_t* )calloc(thread_n, 4);
seedn = (uint16_t* )calloc(thread_n, 2);
#endif
read_bit_1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
read_bit_2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
read_val_1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
read_val_2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
read_val1 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
read_val1[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
read_val1[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
read_val1[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
read_val2 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
read_val2[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
read_val2[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
read_val2[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
#ifdef QUAL_FILT_LV
qual_filt_lv1 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
qual_filt_lv1[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
qual_filt_lv1[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
qual_filt_lv1[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
qual_filt_lv2 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
qual_filt_lv2[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
qual_filt_lv2[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
qual_filt_lv2[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
#endif
#ifdef MAPPING_QUALITY
mp_subs1 = (float*** )calloc(thread_n, sizeof(float** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
mp_subs1[r_i] = (float** )calloc(2, sizeof(float* ));
mp_subs1[r_i][0] = (float* )calloc(readlen_max, sizeof(float));
mp_subs1[r_i][1] = (float* )calloc(readlen_max, sizeof(float));
}
mp_subs2 = (float*** )calloc(thread_n, sizeof(float** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
mp_subs2[r_i] = (float** )calloc(2, sizeof(float* ));
mp_subs2[r_i][0] = (float* )calloc(readlen_max, sizeof(float));
mp_subs2[r_i][1] = (float* )calloc(readlen_max, sizeof(float));
}
sub_t = (float* )calloc(thread_n, sizeof(float ));
#endif
#ifdef PR_COV_FILTER
cov_filt_f = (uint8_t* )calloc(thread_n, 1);
#endif
//end thread gloabl value
#endif
fprintf(stderr, "successfully allocate memory\n");
InitiateLVCompute(L, thread_n);
//for pthread read input
fprintf(stderr, "Load seq input memory\n");
seqio = (seq_io* )calloc(read_in, sizeof(seq_io));
char** read_seq1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
read_seq1_buffer[r_i] = (char* )calloc(readlen_max, 1);
char** read_seq2_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
read_seq2_buffer[r_i] = (char* )calloc(readlen_max, 1);
char** name_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
name_buffer[r_i] = (char* )calloc(readlen_name, 1);
char** name_buffer_other= (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
name_buffer_other[r_i] = (char* )calloc(readlen_name, 1);
qual1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
qual1_buffer[r_i] = (char* )calloc(readlen_max, 1);
qual2_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
qual2_buffer[r_i] = (char* )calloc(readlen_max, 1);
#ifdef FIX_SA
read_rev_buffer_1 = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
read_rev_buffer_1[r_i] = (char* )calloc(readlen_max, 1);
#endif
#ifdef OUTPUT_ARR
read_rev_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
read_rev_buffer[r_i] = (char* )calloc(readlen_max, 1);
pr_cigar1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
pr_cigar1_buffer[r_i] = (char* )calloc(cigar_max_n, 1);
pr_cigar2_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
pr_cigar2_buffer[r_i] = (char* )calloc(cigar_max_n, 1);
chr_res_buffer = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
chr_res_buffer[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
#ifdef FIX_SV
chr_res_buffer1 = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
chr_res_buffer1[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
chr_res_buffer2 = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
chr_res_buffer2[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
#endif
xa_d1s_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
xa_d1s_buffer[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
xa_d2s_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
xa_d2s_buffer[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
sam_pos1s_buffer = (uint32_t** )calloc(read_in, sizeof(uint32_t* ));
for(r_i = 0; r_i < read_in; r_i++)
sam_pos1s_buffer[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
sam_pos2s_buffer = (uint32_t** )calloc(read_in, sizeof(uint32_t* ));
for(r_i = 0; r_i < read_in; r_i++)
sam_pos2s_buffer[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
lv_re1s_buffer = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
lv_re1s_buffer[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
lv_re2s_buffer = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
lv_re2s_buffer[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
#ifdef PR_SINGLE
chr_res1_buffer = (uint8_t** )calloc(read_in, sizeof(uint8_t* ));
for(r_i = 0; r_i < read_in; r_i++)
chr_res1_buffer[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
chr_res2_buffer = (uint8_t** )calloc(read_in, sizeof(uint8_t* ));
for(r_i = 0; r_i < read_in; r_i++)
chr_res2_buffer[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
xa_ds1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
xa_ds1_buffer[r_i] = (char* )calloc(pr_single_outputn, 1);
xa_ds2_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
xa_ds2_buffer[r_i] = (char* )calloc(pr_single_outputn, 1);
lv_res1_buffer = (uint8_t** )calloc(read_in, sizeof(uint8_t* ));
for(r_i = 0; r_i < read_in; r_i++)
lv_res1_buffer[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
lv_res2_buffer = (uint8_t** )calloc(read_in, sizeof(uint8_t* ));
for(r_i = 0; r_i < read_in; r_i++)
lv_res2_buffer[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
sam_poss1_buffer = (uint32_t** )calloc(read_in, sizeof(uint32_t* ));
for(r_i = 0; r_i < read_in; r_i++)
sam_poss1_buffer[r_i] = (uint32_t* )calloc(pr_single_outputn, 4);
sam_poss2_buffer = (uint32_t** )calloc(read_in, sizeof(uint32_t* ));
for(r_i = 0; r_i < read_in; r_i++)
sam_poss2_buffer[r_i] = (uint32_t* )calloc(pr_single_outputn, 4);
#endif
#endif
#ifdef KSW_ALN_PAIR
ali_ref_seq2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
ali_ref_seq2[r_i] = (char* )calloc(readlen_max + 64, 1);
read_char2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
read_char2[r_i] = (char* )calloc(readlen_max + 32, 1);
op_dm_kl1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_kl1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_kr1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_kr1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_kl2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_kl2[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_kr2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_kr2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_kl1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_kl1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_kr1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_kr1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_kl2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_kl2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_kr2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_kr2[r_i] = (int* )calloc(cus_max_output_ali, 4);
mat = (int8_t*)calloc(25, sizeof(int8_t));
for (l = k1 = 0; l < 4; ++l)
{
for (m = 0; m < 4; ++m) mat[k1++] = l == m ? mat_score : -mis_score; /* weight_match : -weight_mismatch */
mat[k1++] = -1; // ambiguous base
}
for (m = 0; m < 5; ++m) mat[k1++] = 0;
#endif
#ifdef PAIR_RANDOM
for(r_i = 0; r_i < thread_n; r_i++)
{
read_bit_pr[r_i][0] = read_bit1[r_i][0];
read_bit_pr[r_i][1] = read_bit2[r_i][1];
read_bit_pr[r_i][2] = read_bit2[r_i][0];
read_bit_pr[r_i][3] = read_bit1[r_i][1];
read_val_pr[r_i][0] = read_val1[r_i][0];
read_val_pr[r_i][1] = read_val2[r_i][1];
read_val_pr[r_i][2] = read_val2[r_i][0];
read_val_pr[r_i][3] = read_val1[r_i][1];
}
#endif
end = clock();
t = (double)(end - start) / CLOCKS_PER_SEC;
fprintf(stderr, "%lf seconds is used for allocating memory\n", t);
//write .sam head into result file
if(flag_std)
for(r_i = 1; r_i < chr_file_n; r_i++)
printf("@SQ\tSN:%s\tLN:%u\n", chr_names[r_i], (uint32_t )(chr_end_n[r_i] - chr_end_n[r_i - 1]));
else
for(r_i = 1; r_i < chr_file_n; r_i++)
fprintf(fp_sam, "@SQ\tSN:%s\tLN:%u\n", chr_names[r_i], (uint32_t )(chr_end_n[r_i] - chr_end_n[r_i - 1]));
#ifdef RD_FILED
if(flag_std)
{
printf("@RG\tID:L1\tPU:SC_1_10\tLB:SC_1\tSM:NA12878\n");
printf("@RG\tID:L2\tPU:SC_2_12\tLB:SC_2\tSM:NA12878\n");
}else{
fprintf(fp_sam, "@RG\tID:L1\tPU:SC_1_10\tLB:SC_1\tSM:NA12878\n");
fprintf(fp_sam, "@RG\tID:L2\tPU:SC_2_12\tLB:SC_2\tSM:NA12878\n");
}
#endif
fprintf(stderr, "begin reading fastq pair-end reads and doing alignment\n");
//fflush(stdout);
#ifdef R_W_LOCK
pthread_rwlock_init(&rwlock, NULL);
int seqii_i = 0;
#endif
double dtime = omp_get_wtime(); //value in seconds
int read_length_tmp1 = 0;
int read_length_tmp2 = 0;
char tmp_pos_ch;
#ifdef FIX_SA
uint16_t xa_n_p1_tmp = 0;
uint16_t sam_seq_i = 0;
char sam_seq1[MAX_READLEN] = {};
uint16_t flag_tmp = 0;
char* seq_tmp = NULL;
char* read_tmp = NULL;
char* qual_tmp = NULL;
#endif
while ((kr1 > 0) && (kr2 > 0))
{
for(seqii = 0; (seqii < read_in) && (((kr1 = kseq_read(seq1)) > 0) && ((kr2 = kseq_read(seq2)) > 0)); seqii++) //((kr1 > 0) && (kr2 > 0))
{
strncpy(name_buffer[seqii], seq1->name.s, seq1->name.l);
strncpy(name_buffer_other[seqii], seq2->name.s, seq2->name.l);
if((seq1->name.s)[seq1->name.l - 2] == '/')
name_buffer[seqii][seq1->name.l - 2] = '\0';
else name_buffer[seqii][seq1->name.l] = '\0';
if((seq2->name.s)[seq2->name.l - 2] == '/')
name_buffer_other[seqii][seq2->name.l - 2] = '\0';
else name_buffer_other[seqii][seq2->name.l] = '\0';
if(seq1->seq.l > readlen_max)
{
seqio[seqii].read_length1 = readlen_max;
seqio[seqii].length_h1 = seq1->seq.l - readlen_max;
}
else
{
seqio[seqii].read_length1 = seq1->seq.l;
seqio[seqii].length_h1 = 0;
}
if(seq2->seq.l > readlen_max)
{
seqio[seqii].read_length2 = readlen_max;
seqio[seqii].length_h2 = seq2->seq.l - readlen_max;
}
else
{
seqio[seqii].read_length2 = seq2->seq.l;
seqio[seqii].length_h2 = 0;
}
read_length_tmp1 = seqio[seqii].read_length1;
read_length_tmp2 = seqio[seqii].read_length2;
strncpy(read_seq1_buffer[seqii], seq1->seq.s, read_length_tmp1);
strncpy(read_seq2_buffer[seqii], seq2->seq.s, read_length_tmp2);
read_seq1_buffer[seqii][read_length_tmp1] = '\0';
read_seq2_buffer[seqii][read_length_tmp2] = '\0';
strncpy(qual1_buffer[seqii], seq1->qual.s, read_length_tmp1);
strncpy(qual2_buffer[seqii], seq2->qual.s, read_length_tmp2);
qual1_buffer[seqii][read_length_tmp1] = '\0';
qual2_buffer[seqii][read_length_tmp2] = '\0';
seqio[seqii].read_seq1 = read_seq1_buffer[seqii];
seqio[seqii].read_seq2 = read_seq2_buffer[seqii];
seqio[seqii].name = name_buffer[seqii];
seqio[seqii].name_other = name_buffer_other[seqii];
seqio[seqii].qual1 = qual1_buffer[seqii];
seqio[seqii].qual2 = qual2_buffer[seqii];
}
if(thread_n <= 1)
{
#ifdef R_W_LOCK
for(seqii_i = 0; seqii_i < seqii; seqii_i++)
seed_ali_core(seqii_i, 0);
#else
seed_ali_core(seqii, 0);
#endif
}
else
{
pthread_t* tid;
thread_ali_t* data;
pthread_attr_t attr;
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
data = (thread_ali_t* )calloc(thread_n, sizeof(thread_ali_t ));
tid = (pthread_t* )calloc(thread_n, sizeof(pthread_t ));
#ifdef R_W_LOCK
read_seq = 0;
#endif
for(r_i = 0; r_i < thread_n; ++r_i)
{
data[r_i].tid = r_i;
data[r_i].seqn = seqii;
pthread_create(&tid[r_i], &attr, worker, data + r_i);
}
for(r_i = 0; r_i < thread_n; ++r_i) pthread_join(tid[r_i], 0);
free(data);
free(tid);
}
if(flag_std)
{
//output
#ifdef OUTPUT_ARR
for(seqi = 0; seqi < seqii; seqi++)
{
if((seqio[seqi].flag1 == 77) && (seqio[seqi].flag2 == 141)) tmp_pos_ch = '*';
else tmp_pos_ch = '=';
if(seqio[seqi].length_h1 == 0)
{
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].cross, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
else
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, tmp_pos_ch, seqio[seqi].pos1, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
if(seqio[seqi].xa_n_p1 > 0)
{
printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p1; v_cnt_i++)
printf("%s,%c%u,%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d1s[v_cnt_i], seqio[seqi].sam_pos1s[v_cnt_i], seqio[seqi].cigar_p1s[v_cnt_i], seqio[seqi].lv_re1s[v_cnt_i]); }
#ifdef PR_SINGLE
if(seqio[seqi].xa_n1 > 0)
{
if((seqio[seqi].xa_n_p1 == 0) && (seqio[seqi].xa_n1 > 0)) printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n1; v_cnt_i++)
printf("%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res1[v_cnt_i]], seqio[seqi].xa_ds1[v_cnt_i], seqio[seqi].sam_poss1[v_cnt_i], seqio[seqi].read_length1, seqio[seqi].lv_res1[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x1 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p1;
printf("\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x1; v_cnt_i++)
{
printf("%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s1[v_cnt_i]], seqio[seqi].sam_pos1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc1, seqio[seqi].lv_re1s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
printf("\tNM:i:%u\tRG:Z:L1\n", seqio[seqi].nm1);
#else
printf("\tNM:i:%u\n", seqio[seqi].nm1);
#endif
}
else
{
sprintf(h_chars, "%uH", seqio[seqi].length_h1);
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, h_chars, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].cross, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
else
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, h_chars, tmp_pos_ch, seqio[seqi].pos1, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
if(seqio[seqi].xa_n_p1 > 0)
{
printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p1; v_cnt_i++)
{
printf("%s,%c%u,%s%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d1s[v_cnt_i], seqio[seqi].sam_pos1s[v_cnt_i], seqio[seqi].cigar_p1s[v_cnt_i], h_chars, seqio[seqi].lv_re1s[v_cnt_i]);
}
}
printf("NM:i:%u\t", seqio[seqi].nm1);
#ifdef PR_SINGLE
if(seqio[seqi].xa_n1 > 0)
{
if((seqio[seqi].xa_n_p1 == 0) && (seqio[seqi].xa_n1 > 0)) printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n1; v_cnt_i++)
printf("%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res1[v_cnt_i]], seqio[seqi].xa_ds1[v_cnt_i], seqio[seqi].sam_poss1[v_cnt_i], seqio[seqi].read_length1, seqio[seqi].lv_res1[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x1 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p1;
printf("\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x1; v_cnt_i++)
{
printf("%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s1[v_cnt_i]], seqio[seqi].sam_pos1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc1, seqio[seqi].lv_re1s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
printf("\tNM:i:%u\tRG:Z:L1\n", seqio[seqi].nm1);
#else
printf("\tNM:i:%u\n", seqio[seqi].nm1);
#endif
}
#ifdef FIX_SV
#ifndef FIX_SA
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x1; v_cnt_i++)
{
if(seqio[seqi].xa_d1s[v_cnt_i + seqio[seqi].xa_n_p1] == '+')
{
flag_tmp = 2145;
seq_tmp = seqio[seqi].read_seq1;
}
else
{
flag_tmp = 2129;
read_tmp = seqio[seqi].read_seq1;
for(sam_seq_i = 0; sam_seq_i < seqio[seqi].read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[read_tmp[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
seq_tmp = sam_seq1;
}
qual_tmp = seqio[seqi].qual1;
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%d\t%s\t%s\tNM:i:%u\tRG:Z:L1\n",
seqio[seqi].name, flag_tmp, chr_names[seqio[seqi].chr_res_s1[v_cnt_i]], seqio[seqi].sam_pos1s[v_cnt_i + seqio[seqi].xa_n_p1],
seqio[seqi].qualc1, seqio[seqi].cigar_p1s[v_cnt_i + seqio[seqi].xa_n_p1], tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].pos2 - seqio[seqi].sam_pos1s[v_cnt_i + seqio[seqi].xa_n_p1], seq_tmp,
qual_tmp, seqio[seqi].lv_re1s[v_cnt_i + seqio[seqi].xa_n_p1]
);
}
#endif
#endif
if(seqio[seqi].length_h2 == 0)
{
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, tmp_pos_ch, seqio[seqi].pos1, -seqio[seqi].cross, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
else
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
if(seqio[seqi].xa_n_p2 > 0)
{
printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p2; v_cnt_i++)
printf("%s,%c%u,%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d2s[v_cnt_i], seqio[seqi].sam_pos2s[v_cnt_i], seqio[seqi].cigar_p2s[v_cnt_i], seqio[seqi].lv_re2s[v_cnt_i]);
}
#ifdef PR_SINGLE
if(seqio[seqi].xa_n2 > 0)
{
if((seqio[seqi].xa_n_p2 == 0) && (seqio[seqi].xa_n2 > 0)) printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n2; v_cnt_i++)
printf("%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res2[v_cnt_i]], seqio[seqi].xa_ds2[v_cnt_i], seqio[seqi].sam_poss2[v_cnt_i], seqio[seqi].read_length2, seqio[seqi].lv_res2[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x2 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p2;
printf("\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x2; v_cnt_i++)
{
printf("%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s2[v_cnt_i]], seqio[seqi].sam_pos2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc2, seqio[seqi].lv_re2s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
printf("\tNM:i:%u\tRG:Z:L2\n", seqio[seqi].nm2);
#else
printf("\tNM:i:%u\n", seqio[seqi].nm2);
#endif
}
else
{
sprintf(h_chars, "%uH", seqio[seqi].length_h2);
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, h_chars, tmp_pos_ch, seqio[seqi].pos1, -seqio[seqi].cross, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
else
{
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, h_chars, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
if(seqio[seqi].xa_n_p2 > 0)
{
printf( "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p2; v_cnt_i++)
{
printf("%s,%c%u,%s%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d2s[v_cnt_i], seqio[seqi].sam_pos2s[v_cnt_i], seqio[seqi].cigar_p2s[v_cnt_i], h_chars, seqio[seqi].lv_re2s[v_cnt_i]);
}
}
#ifdef PR_SINGLE
if(seqio[seqi].xa_n2 > 0)
{
if((seqio[seqi].xa_n_p2 == 0) && (seqio[seqi].xa_n2 > 0)) printf("\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n2; v_cnt_i++)
printf("%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res2[v_cnt_i]], seqio[seqi].xa_ds2[v_cnt_i], seqio[seqi].sam_poss2[v_cnt_i], seqio[seqi].read_length2, seqio[seqi].lv_res2[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x2 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p2;
printf("\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x2; v_cnt_i++)
{
printf("%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s2[v_cnt_i]], seqio[seqi].sam_pos2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc2, seqio[seqi].lv_re2s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
printf("\tNM:i:%u\tRG:Z:L2\n", seqio[seqi].nm2);
#else
printf("\tNM:i:%u\n", seqio[seqi].nm2);
#endif
}
#ifdef FIX_SV
#ifndef FIX_SA
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x2; v_cnt_i++)
{
if(seqio[seqi].xa_d2s[v_cnt_i + seqio[seqi].xa_n_p2] == '+')
{
flag_tmp = 2209;
seq_tmp = seqio[seqi].read_seq2;
}
else
{
flag_tmp = 2193;
read_tmp = seqio[seqi].read_seq2;
for(sam_seq_i = 0; sam_seq_i < seqio[seqi].read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[read_tmp[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
seq_tmp = sam_seq1;
}
qual_tmp = seqio[seqi].qual2;
//seqio[seqi].read_seq1
//read_rev_buffer[seqi]
printf("%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%d\t%s\t%s\tNM:i:%u\tRG:Z:L2\n",
seqio[seqi].name_other, flag_tmp, chr_names[seqio[seqi].chr_res_s2[v_cnt_i]], seqio[seqi].sam_pos2s[v_cnt_i + seqio[seqi].xa_n_p2],
seqio[seqi].qualc2, seqio[seqi].cigar_p2s[v_cnt_i + seqio[seqi].xa_n_p2], tmp_pos_ch, seqio[seqi].sam_pos2s[v_cnt_i + seqio[seqi].xa_n_p2], seqio[seqi].sam_pos2s[v_cnt_i + seqio[seqi].xa_n_p2] - seqio[seqi].pos1, seq_tmp,
qual_tmp, seqio[seqi].lv_re2s[v_cnt_i + seqio[seqi].xa_n_p2]
);
}
#endif
#endif
}
#endif
}
else
{
//output
#ifdef OUTPUT_ARR
for(seqi = 0; seqi < seqii; seqi++)
{
if((seqio[seqi].flag1 == 77) && (seqio[seqi].flag2 == 141)) tmp_pos_ch = '*';
else tmp_pos_ch = '=';
if(seqio[seqi].length_h1 == 0)
{
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].cross, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
else
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, tmp_pos_ch, seqio[seqi].pos1, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
if(seqio[seqi].xa_n_p1 > 0)
{
fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p1; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d1s[v_cnt_i], seqio[seqi].sam_pos1s[v_cnt_i], seqio[seqi].cigar_p1s[v_cnt_i], seqio[seqi].lv_re1s[v_cnt_i]);
}
#ifdef PR_SINGLE
if(seqio[seqi].xa_n1 > 0)
{
if((seqio[seqi].xa_n_p1 == 0) && (seqio[seqi].xa_n1 > 0)) fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n1; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res1[v_cnt_i]], seqio[seqi].xa_ds1[v_cnt_i], seqio[seqi].sam_poss1[v_cnt_i], seqio[seqi].read_length1, seqio[seqi].lv_res1[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x1 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p1;
fprintf(fp_sam, "\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x1; v_cnt_i++)
{
fprintf(fp_sam, "%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s1[v_cnt_i]], seqio[seqi].sam_pos1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc1, seqio[seqi].lv_re1s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
fprintf(fp_sam, "\tNM:i:%u\tRG:Z:L1\n", seqio[seqi].nm1);
#else
fprintf(fp_sam, "\tNM:i:%u\n", seqio[seqi].nm1);
#endif
}
else
{
sprintf(h_chars, "%uH", seqio[seqi].length_h1);
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, h_chars, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].cross, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
else
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re1], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, h_chars, tmp_pos_ch, seqio[seqi].pos1, seqio[seqi].seq1,
seqio[seqi].qual1
);
}
if(seqio[seqi].xa_n_p1 > 0)
{
fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p1; v_cnt_i++)
{
fprintf(fp_sam, "%s,%c%u,%s%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d1s[v_cnt_i], seqio[seqi].sam_pos1s[v_cnt_i], seqio[seqi].cigar_p1s[v_cnt_i], h_chars, seqio[seqi].lv_re1s[v_cnt_i]);
}
}
fprintf(fp_sam, "NM:i:%u\t", seqio[seqi].nm1);
#ifdef PR_SINGLE
if(seqio[seqi].xa_n1 > 0)
{
if((seqio[seqi].xa_n_p1 == 0) && (seqio[seqi].xa_n1 > 0)) fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n1; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res1[v_cnt_i]], seqio[seqi].xa_ds1[v_cnt_i], seqio[seqi].sam_poss1[v_cnt_i], seqio[seqi].read_length1, seqio[seqi].lv_res1[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x1 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p1;
fprintf(fp_sam, "\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x1; v_cnt_i++)
{
fprintf(fp_sam, "%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s1[v_cnt_i]], seqio[seqi].sam_pos1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p1s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc1, seqio[seqi].lv_re1s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
fprintf(fp_sam, "\tNM:i:%u\tRG:Z:L1\n", seqio[seqi].nm1);
#else
fprintf(fp_sam, "\tNM:i:%u\n", seqio[seqi].nm1);
#endif
}
#ifdef FIX_SV
#ifndef FIX_SA
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x1; v_cnt_i++)
{
if(seqio[seqi].xa_d1s[v_cnt_i + seqio[seqi].xa_n_p1] == '+')
{
flag_tmp = 2145;
seq_tmp = seqio[seqi].read_seq1;
}
else
{
flag_tmp = 2129;
read_tmp = seqio[seqi].read_seq1;
for(sam_seq_i = 0; sam_seq_i < seqio[seqi].read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[read_tmp[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
seq_tmp = sam_seq1;
}
qual_tmp = seqio[seqi].qual1;
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%d\t%s\t%s\tNM:i:%u\tRG:Z:L1\n",
seqio[seqi].name, flag_tmp, chr_names[seqio[seqi].chr_res_s1[v_cnt_i]], seqio[seqi].sam_pos1s[v_cnt_i + seqio[seqi].xa_n_p1],
seqio[seqi].qualc1, seqio[seqi].cigar_p1s[v_cnt_i + seqio[seqi].xa_n_p1], tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].pos2 - seqio[seqi].sam_pos1s[v_cnt_i + seqio[seqi].xa_n_p1], seq_tmp,
qual_tmp, seqio[seqi].lv_re1s[v_cnt_i + seqio[seqi].xa_n_p1]
);
}
#endif
#endif
if(seqio[seqi].length_h2 == 0)
{
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, tmp_pos_ch, seqio[seqi].pos1, -seqio[seqi].cross, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
else
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
if(seqio[seqi].xa_n_p2 > 0)
{
fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p2; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d2s[v_cnt_i], seqio[seqi].sam_pos2s[v_cnt_i], seqio[seqi].cigar_p2s[v_cnt_i], seqio[seqi].lv_re2s[v_cnt_i]);
}
#ifdef PR_SINGLE
if(seqio[seqi].xa_n2 > 0)
{
if((seqio[seqi].xa_n_p2 == 0) && (seqio[seqi].xa_n2 > 0)) fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n2; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res2[v_cnt_i]], seqio[seqi].xa_ds2[v_cnt_i], seqio[seqi].sam_poss2[v_cnt_i], seqio[seqi].read_length2, seqio[seqi].lv_res2[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x2 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p2;
fprintf(fp_sam, "\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x2; v_cnt_i++)
{
fprintf(fp_sam, "%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s2[v_cnt_i]], seqio[seqi].sam_pos2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc2, seqio[seqi].lv_re2s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
fprintf(fp_sam, "\tNM:i:%u\tRG:Z:L2\n", seqio[seqi].nm2);
#else
fprintf(fp_sam, "\tNM:i:%u\n", seqio[seqi].nm2);
#endif
}
else
{
sprintf(h_chars, "%uH", seqio[seqi].length_h2);
if(seqio[seqi].chr_re1 == seqio[seqi].chr_re2)
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t%"PRId64"\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, h_chars, tmp_pos_ch, seqio[seqi].pos1, -seqio[seqi].cross, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
else
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t%c\t%"PRId64"\t0\t%s\t%s",
seqio[seqi].name_other, seqio[seqi].flag2, chr_names[seqio[seqi].chr_re2], seqio[seqi].pos2,
seqio[seqi].qualc2, seqio[seqi].cigar2, h_chars, tmp_pos_ch, seqio[seqi].pos2, seqio[seqi].seq2,
seqio[seqi].qual2
);
}
if(seqio[seqi].xa_n_p2 > 0)
{
fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p2; v_cnt_i++)
{
fprintf(fp_sam, "%s,%c%u,%s%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d2s[v_cnt_i], seqio[seqi].sam_pos2s[v_cnt_i], seqio[seqi].cigar_p2s[v_cnt_i], h_chars, seqio[seqi].lv_re2s[v_cnt_i]);
}
}
#ifdef PR_SINGLE
if(seqio[seqi].xa_n2 > 0)
{
if((seqio[seqi].xa_n_p2 == 0) && (seqio[seqi].xa_n2 > 0)) fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n2; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%uM,%u;", chr_names[seqio[seqi].chr_res2[v_cnt_i]], seqio[seqi].xa_ds2[v_cnt_i], seqio[seqi].sam_poss2[v_cnt_i], seqio[seqi].read_length2, seqio[seqi].lv_res2[v_cnt_i]);
}
#endif
#ifdef FIX_SA
if(seqio[seqi].xa_n_x2 > 0)
{
xa_n_p1_tmp = seqio[seqi].xa_n_p2;
fprintf(fp_sam, "\tSA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x2; v_cnt_i++)
{
fprintf(fp_sam, "%s,%u,%c,%s,%u,%d;", chr_names[seqio[seqi].chr_res_s2[v_cnt_i]], seqio[seqi].sam_pos2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].xa_d2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].cigar_p2s[v_cnt_i + xa_n_p1_tmp], seqio[seqi].qualc2, seqio[seqi].lv_re2s[v_cnt_i + xa_n_p1_tmp]);
}
}
#endif
#ifdef RD_FILED
fprintf(fp_sam, "\tNM:i:%u\tRG:Z:L2\n", seqio[seqi].nm2);
#else
fprintf(fp_sam, "\tNM:i:%u\n", seqio[seqi].nm2);
#endif
}
#ifdef FIX_SV
#ifndef FIX_SA
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_x2; v_cnt_i++)
{
if(seqio[seqi].xa_d2s[v_cnt_i + seqio[seqi].xa_n_p2] == '+')
{
flag_tmp = 2209;
seq_tmp = seqio[seqi].read_seq2;
}
else
{
flag_tmp = 2193;
read_tmp = seqio[seqi].read_seq2;
for(sam_seq_i = 0; sam_seq_i < seqio[seqi].read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[read_tmp[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
seq_tmp = sam_seq1;
}
qual_tmp = seqio[seqi].qual2;
//seqio[seqi].read_seq1
//read_rev_buffer[seqi]
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t%c\t%"PRId64"\t%d\t%s\t%s\tNM:i:%u\tRG:Z:L2\n",
seqio[seqi].name_other, flag_tmp, chr_names[seqio[seqi].chr_res_s2[v_cnt_i]], seqio[seqi].sam_pos2s[v_cnt_i + seqio[seqi].xa_n_p2],
seqio[seqi].qualc2, seqio[seqi].cigar_p2s[v_cnt_i + seqio[seqi].xa_n_p2], tmp_pos_ch, seqio[seqi].sam_pos2s[v_cnt_i + seqio[seqi].xa_n_p2], seqio[seqi].sam_pos2s[v_cnt_i + seqio[seqi].xa_n_p2] - seqio[seqi].pos1, seq_tmp,
qual_tmp, seqio[seqi].lv_re2s[v_cnt_i + seqio[seqi].xa_n_p2]
);
}
#endif
#endif
}
#endif
}
#ifdef POST_DEBUG
printf("print end\n");
#endif
#ifdef OUTPUT_ARR
for(seqi = 0; seqi < seqii; seqi++)
{
if(seqio[seqi].v_cnt > 0)
{
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p1; v_cnt_i++)
free(seqio[seqi].cigar_p1s[v_cnt_i]);
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n_p2; v_cnt_i++)
free(seqio[seqi].cigar_p2s[v_cnt_i]);
}
}
#endif
}
dtime = omp_get_wtime() - dtime;
fprintf(stderr, "%lf seconds is used in mapping\n", dtime);
fflush(stdout);
#ifdef R_W_LOCK
pthread_rwlock_destroy(&rwlock);
#endif
if(flag_std == 0)
fclose(fp_sam);
kseq_destroy(seq1);
gzclose(fp1);
kseq_destroy(seq2);
gzclose(fp2);
#ifdef STA_SEED
fclose(fp_read);
fclose(fp_seed);
#endif
#ifdef PTHREAD_USE
fprintf(stderr, "free memory\n");
if(g_low != NULL) free(g_low);
if(r_low != NULL) free(r_low);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedm[r_i] != NULL) free(seedm[r_i]);
if(seedm != NULL) free(seedm);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedu[r_i] != NULL) free(seedu[r_i]);
if(seedu != NULL) free(seedu);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedsets[r_i] != NULL) free(seedsets[r_i]);
if(seedsets != NULL) free(seedsets);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_off[r_i] != NULL) free(seed_set_off[r_i]);
if(seed_set_off != NULL) free(seed_set_off);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_pos[0][0][r_i] != NULL) free(seed_set_pos[0][0][r_i]);
if(seed_set_pos[0][0] != NULL) free(seed_set_pos[0][0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_pos[0][1][r_i] != NULL) free(seed_set_pos[0][1][r_i]);
if(seed_set_pos[0][1] != NULL) free(seed_set_pos[0][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_pos[1][0][r_i] != NULL) free(seed_set_pos[1][0][r_i]);
if(seed_set_pos[1][0] != NULL) free(seed_set_pos[1][0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_pos[1][1][r_i] != NULL) free(seed_set_pos[1][1][r_i]);
if(seed_set_pos[1][1] != NULL) free(seed_set_pos[1][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpa1[0][r_i] != NULL) free(seedpa1[0][r_i]);
if(seedpa1[0] != NULL) free(seedpa1[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpa1[1][r_i] != NULL) free(seedpa1[1][r_i]);
if(seedpa1[1] != NULL) free(seedpa1[1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpa2[0][r_i] != NULL) free(seedpa2[0][r_i]);
if(seedpa2[0] != NULL) free(seedpa2[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpa2[1][r_i] != NULL) free(seedpa2[1][r_i]);
if(seedpa2[1] != NULL) free(seedpa2[1]);
#ifdef ALTER_DEBUG
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_length_arr[r_i] != NULL) free(seed_length_arr[r_i]);
if(seed_length_arr != NULL) free(seed_length_arr);
if(rep_go != NULL) free(rep_go);
#endif
#ifdef REDUCE_ANCHOR
for(r_i = 0; r_i < thread_n; r_i++)
if(poses1[r_i] != NULL) free(poses1[r_i]);
if(poses1 != NULL) free(poses1);
for(r_i = 0; r_i < thread_n; r_i++)
if(poses2[r_i] != NULL) free(poses2[r_i]);
if(poses2 != NULL) free(poses2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ls1[r_i] != NULL) free(ls1[r_i]);
if(ls1 != NULL) free(ls1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ls2[r_i] != NULL) free(ls2[r_i]);
if(ls2 != NULL) free(ls2);
for(r_i = 0; r_i < thread_n; r_i++)
if(rs1[r_i] != NULL) free(rs1[r_i]);
if(rs1 != NULL) free(rs1);
for(r_i = 0; r_i < thread_n; r_i++)
if(rs2[r_i] != NULL) free(rs2[r_i]);
if(rs2 != NULL) free(rs2);
for(r_i = 0; r_i < thread_n; r_i++)
if(rcs1[r_i] != NULL) free(rcs1[r_i]);
if(rcs1 != NULL) free(rcs1);
for(r_i = 0; r_i < thread_n; r_i++)
if(rcs2[r_i] != NULL) free(rcs2[r_i]);
if(rcs2 != NULL) free(rcs2);
#endif
for(r_i = 0; r_i < thread_n; r_i++)
if(op_vector_pos1[r_i] != NULL) free(op_vector_pos1[r_i]);
if(op_vector_pos1 != NULL) free(op_vector_pos1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_vector_pos2[r_i] != NULL) free(op_vector_pos2[r_i]);
if(op_vector_pos2 != NULL) free(op_vector_pos2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_vector_pos1[r_i] != NULL) free(ops_vector_pos1[r_i]);
if(ops_vector_pos1 != NULL) free(ops_vector_pos1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_vector_pos2[r_i] != NULL) free(ops_vector_pos2[r_i]);
if(ops_vector_pos2 != NULL) free(ops_vector_pos2);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_l1[r_i] != NULL) free(op_dm_l1[r_i]);
if(op_dm_l1 != NULL) free(op_dm_l1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_r1[r_i] != NULL) free(op_dm_r1[r_i]);
if(op_dm_r1 != NULL) free(op_dm_r1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_l2[r_i] != NULL) free(op_dm_l2[r_i]);
if(op_dm_l2 != NULL) free(op_dm_l2);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_r2[r_i] != NULL) free(op_dm_r2[r_i]);
if(op_dm_r2 != NULL) free(op_dm_r2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_l1[r_i] != NULL) free(ops_dm_l1[r_i]);
if(ops_dm_l1 != NULL) free(ops_dm_l1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_r1[r_i] != NULL) free(ops_dm_r1[r_i]);
if(ops_dm_r1 != NULL) free(ops_dm_r1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_l2[r_i] != NULL) free(ops_dm_l2[r_i]);
if(ops_dm_l2 != NULL) free(ops_dm_l2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_r2[r_i] != NULL) free(ops_dm_r2[r_i]);
if(ops_dm_r2 != NULL) free(ops_dm_r2);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_ex1[r_i] != NULL) free(op_dm_ex1[r_i]);
if(op_dm_ex1 != NULL) free(op_dm_ex1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_ex2[r_i] != NULL) free(op_dm_ex2[r_i]);
if(op_dm_ex2 != NULL) free(op_dm_ex2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_ex1[r_i] != NULL) free(ops_dm_ex1[r_i]);
if(ops_dm_ex1 != NULL) free(ops_dm_ex1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_ex2[r_i] != NULL) free(ops_dm_ex2[r_i]);
if(ops_dm_ex2 != NULL) free(ops_dm_ex2);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < cus_max_output_ali; m++)
if(op_vector_seq1[r_i][m] != NULL) free(op_vector_seq1[r_i][m]);
if(op_vector_seq1[r_i] != NULL) free(op_vector_seq1[r_i]);
}
if(op_vector_seq1 != NULL) free(op_vector_seq1);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < cus_max_output_ali; m++)
if(op_vector_seq2[r_i][m] != NULL) free(op_vector_seq2[r_i][m]);
if(op_vector_seq2[r_i] != NULL) free(op_vector_seq2[r_i]);
}
if(op_vector_seq2 != NULL) free(op_vector_seq2);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < cus_max_output_ali; m++)
if(ops_vector_seq1[r_i][m] != NULL) free(ops_vector_seq1[r_i][m]);
if(ops_vector_seq1[r_i] != NULL) free(ops_vector_seq1[r_i]);
}
if(ops_vector_seq1 != NULL) free(ops_vector_seq1);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < cus_max_output_ali; m++)
if(ops_vector_seq2[r_i][m] != NULL) free(ops_vector_seq2[r_i][m]);
if(ops_vector_seq2[r_i] != NULL) free(ops_vector_seq2[r_i]);
}
if(ops_vector_seq2 != NULL) free(ops_vector_seq2);
#ifdef ALT_ALL
for(r_i = 0; r_i < thread_n; r_i++)
if(chr_res[r_i] != NULL) free(chr_res[r_i]);
if(chr_res != NULL) free(chr_res);
for(r_i = 0; r_i < thread_n; r_i++)
if(sam_pos1s[r_i] != NULL) free(sam_pos1s[r_i]);
if(sam_pos1s != NULL) free(sam_pos1s);
for(r_i = 0; r_i < thread_n; r_i++)
if(sam_pos2s[r_i] != NULL) free(sam_pos2s[r_i]);
if(sam_pos2s != NULL) free(sam_pos2s);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if(cigar_p1s[r_i][m] != NULL) free(cigar_p1s[r_i][m]);
if(cigar_p1s[r_i] != NULL) free(cigar_p1s[r_i]);
}
if(cigar_p1s != NULL) free(cigar_p1s);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if(cigar_p2s[r_i][m] != NULL) free(cigar_p2s[r_i][m]);
if(cigar_p2s[r_i] != NULL) free(cigar_p2s[r_i]);
}
if(cigar_p2s != NULL) free(cigar_p2s);
for(r_i = 0; r_i < thread_n; r_i++)
if(xa_d1s[r_i] != NULL) free(xa_d1s[r_i]);
if(xa_d1s != NULL) free(xa_d1s);
for(r_i = 0; r_i < thread_n; r_i++)
if(xa_d2s[r_i] != NULL) free(xa_d2s[r_i]);
if(xa_d2s != NULL) free(xa_d2s);
for(r_i = 0; r_i < thread_n; r_i++)
if(lv_re1s[r_i] != NULL) free(lv_re1s[r_i]);
if(lv_re1s != NULL) free(lv_re1s);
for(r_i = 0; r_i < thread_n; r_i++)
if(lv_re2s[r_i] != NULL) free(lv_re2s[r_i]);
if(lv_re2s != NULL) free(lv_re2s);
#endif
for(r_i = 0; r_i < thread_n; r_i++)
if(op_rc[r_i] != NULL) free(op_rc[r_i]);
if(op_rc != NULL) free(op_rc);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_rc[r_i] != NULL) free(ops_rc[r_i]);
if(ops_rc != NULL) free(ops_rc);
for(r_i = 0; r_i < thread_n; r_i++)
if(ref_seq_tmp1[r_i] != NULL) free(ref_seq_tmp1[r_i]);
if(ref_seq_tmp1 != NULL) free(ref_seq_tmp1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ref_seq_tmp2[r_i] != NULL) free(ref_seq_tmp2[r_i]);
if(ref_seq_tmp2 != NULL) free(ref_seq_tmp2);
for(r_i = 0; r_i < thread_n; r_i++)
if(mat_pos1[r_i] != NULL) free(mat_pos1[r_i]);
if(mat_pos1 != NULL) free(mat_pos1);
for(r_i = 0; r_i < thread_n; r_i++)
if(mat_pos2[r_i] != NULL) free(mat_pos2[r_i]);
if(mat_pos2 != NULL) free(mat_pos2);
for(r_i = 0; r_i < thread_n; r_i++)
if(mat_rc[r_i] != NULL) free(mat_rc[r_i]);
if(mat_rc != NULL) free(mat_rc);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_no1[r_i] != NULL) free(seed_no1[r_i]);
if(seed_no1 != NULL) free(seed_no1);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_no2[r_i] != NULL) free(seed_no2[r_i]);
if(seed_no2 != NULL) free(seed_no2);
#ifdef PAIR_RANDOM
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < readlen_max / pair_ran_intvp; m++)
if(seed_k_pos[r_i][m] != NULL) free(seed_k_pos[r_i][m]);
if(seed_k_pos[r_i] != NULL) free(seed_k_pos[r_i]);
}
if(seed_k_pos != NULL) free(seed_k_pos);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedposk[r_i] != NULL) free(seedposk[r_i]);
if(seedposk != NULL) free(seedposk);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos[0][0][r_i] != NULL) free(seedpos[0][0][r_i]);
if(seedpos[0][0] != NULL) free(seedpos[0][0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos[0][1][r_i] != NULL) free(seedpos[0][1][r_i]);
if(seedpos[0][1] != NULL) free(seedpos[0][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos[1][0][r_i] != NULL) free(seedpos[1][0][r_i]);
if(seedpos[1][0] != NULL) free(seedpos[1][0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos[1][1][r_i] != NULL) free(seedpos[1][1][r_i]);
if(seedpos[1][1] != NULL) free(seedpos[1][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_posf[0][r_i] != NULL) free(seed_posf[0][r_i]);
if(seed_posf[0] != NULL) free(seed_posf[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_posf[1][r_i] != NULL) free(seed_posf[1][r_i]);
if(seed_posf[1] != NULL) free(seed_posf[1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_pos[0][r_i] != NULL) free(seed_single_pos[0][r_i]);
if(seed_single_pos[0] != NULL) free(seed_single_pos[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_pos[1][r_i] != NULL) free(seed_single_pos[1][r_i]);
if(seed_single_pos[1] != NULL) free(seed_single_pos[1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_ld[0][r_i] != NULL) free(seed_single_ld[0][r_i]);
if(seed_single_ld[0] != NULL) free(seed_single_ld[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_ld[1][r_i] != NULL) free(seed_single_ld[1][r_i]);
if(seed_single_ld[1] != NULL) free(seed_single_ld[1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_rd[0][r_i] != NULL) free(seed_single_rd[0][r_i]);
if(seed_single_rd[0] != NULL) free(seed_single_rd[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_rd[1][r_i] != NULL) free(seed_single_rd[1][r_i]);
if(seed_single_rd[1] != NULL) free(seed_single_rd[1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_dm[0][r_i] != NULL) free(seed_single_dm[0][r_i]);
if(seed_single_dm[0] != NULL) free(seed_single_dm[0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_single_dm[1][r_i] != NULL) free(seed_single_dm[1][r_i]);
if(seed_single_dm[1] != NULL) free(seed_single_dm[1]);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < (readlen_max / pair_ran_intvp) * RANDOM_RANGE; m++)
if(seed_single_refs[0][r_i][m] != NULL) free(seed_single_refs[0][r_i][m]);
if(seed_single_refs[0][r_i] != NULL) free(seed_single_refs[0][r_i]);
}
if(seed_single_refs[0] != NULL) free(seed_single_refs[0]);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < (readlen_max / pair_ran_intvp) * RANDOM_RANGE; m++)
if(seed_single_refs[1][r_i][m] != NULL) free(seed_single_refs[1][r_i][m]);
if(seed_single_refs[1][r_i] != NULL) free(seed_single_refs[1][r_i]);
}
if(seed_single_refs[1] != NULL) free(seed_single_refs[1]);
#ifdef PR_SINGLE
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos_mis[0][0][r_i] != NULL) free(seedpos_mis[0][0][r_i]);
if(seedpos_mis[0][0] != NULL) free(seedpos_mis[0][0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos_mis[0][1][r_i] != NULL) free(seedpos_mis[0][1][r_i]);
if(seedpos_mis[0][1] != NULL) free(seedpos_mis[0][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos_mis[1][0][r_i] != NULL) free(seedpos_mis[1][0][r_i]);
if(seedpos_mis[1][0] != NULL) free(seedpos_mis[1][0]);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpos_mis[1][1][r_i] != NULL) free(seedpos_mis[1][1][r_i]);
if(seedpos_mis[1][1] != NULL) free(seedpos_mis[1][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_chr_res1[r_i] != NULL) free(pr_chr_res1[r_i]);
if(pr_chr_res1 != NULL) free(pr_chr_res1);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_sam_pos1[r_i] != NULL) free(pr_sam_pos1[r_i]);
if(pr_sam_pos1 != NULL) free(pr_sam_pos1);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_xa_d1[r_i] != NULL) free(pr_xa_d1[r_i]);
if(pr_xa_d1 != NULL) free(pr_xa_d1);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_lv_re1[r_i] != NULL) free(pr_lv_re1[r_i]);
if(pr_lv_re1 != NULL) free(pr_lv_re1);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_chr_res2[r_i] != NULL) free(pr_chr_res2[r_i]);
if(pr_chr_res2 != NULL) free(pr_chr_res2);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_sam_pos2[r_i] != NULL) free(pr_sam_pos2[r_i]);
if(pr_sam_pos2 != NULL) free(pr_sam_pos2);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_xa_d2[r_i] != NULL) free(pr_xa_d2[r_i]);
if(pr_xa_d2 != NULL) free(pr_xa_d2);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_lv_re2[r_i] != NULL) free(pr_lv_re2[r_i]);
if(pr_lv_re2 != NULL) free(pr_lv_re2);
#endif
#ifdef PAIR_RANDOM_SEED
if(seed_r_dup != NULL) free(seed_r_dup);
if(random_buffer != NULL) free(random_buffer);
#endif
#endif
#ifdef READN_RANDOM_SEED
if(random_buffer_readn) free(random_buffer_readn);
#endif
//thread gloabl value
if(rc_cov_f != NULL) free(rc_cov_f);
for(r_i = 0; r_i < thread_n; r_i++)
if(cov_a_n[r_i] != NULL) free(cov_a_n[r_i]);
if(cov_a_n != NULL) free(cov_a_n);
if(cov_a_n_s != NULL) free(cov_a_n_s);
if(s_uid_f != NULL) free(s_uid_f);
if(min_mis != NULL) free(min_mis);
if(de_m_p != NULL) free(de_m_p);
if(de_m_p_o != NULL) free(de_m_p_o);
if(seed_l != NULL) free(seed_l);
if(max_mismatch1 != NULL) free(max_mismatch1);
if(max_mismatch2 != NULL) free(max_mismatch2);
if(max_mismatch1_single != NULL) free(max_mismatch1_single);
if(max_mismatch2_single != NULL) free(max_mismatch2_single);
#ifdef PR_SINGLE
if(pr_o_f != NULL) free(pr_o_f);
if(seed_re_r != NULL) free(seed_re_r);
#endif
//if(off_start != NULL) free(off_start);
if(end_dis1 != NULL) free(end_dis1);
if(end_dis2 != NULL) free(end_dis2);
if(mat_posi != NULL) free(mat_posi);
#ifdef PAIR_SEED_LENGTH_FILT
if(max_lengtht != NULL) free(max_lengtht);
#endif
#ifdef REDUCE_ANCHOR
for(r_i = 0; r_i < thread_n; r_i++)
if(orders1[r_i] != NULL) free(orders1[r_i]);
if(orders1 != NULL) free(orders1);
for(r_i = 0; r_i < thread_n; r_i++)
if(orders2[r_i] != NULL) free(orders2[r_i]);
if(orders2 != NULL) free(orders2);
for(r_i = 0; r_i < thread_n; r_i++)
if(dms1[r_i] != NULL) free(dms1[r_i]);
if(dms1 != NULL) free(dms1);
for(r_i = 0; r_i < thread_n; r_i++)
if(dms2[r_i] != NULL) free(dms2[r_i]);
if(dms2 != NULL) free(dms2);
#endif
if(dm_op != NULL) free(dm_op);
if(dm_ops != NULL) free(dm_ops);
if(low_mask1 != NULL) free(low_mask1);
if(low_mask2 != NULL) free(low_mask2);
for(r_i = 0; r_i < thread_n; r_i++)
if(pos_add[r_i] != NULL) free(pos_add[r_i]);
if(pos_add != NULL) free(pos_add);
for(r_i = 0; r_i < thread_n; r_i++)
if(cigar_m1[r_i] != NULL) free(cigar_m1[r_i]);
if(cigar_m1 != NULL) free(cigar_m1);
for(r_i = 0; r_i < thread_n; r_i++)
if(cigar_m2[r_i] != NULL) free(cigar_m2[r_i]);
if(cigar_m2 != NULL) free(cigar_m2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ali_ref_seq[r_i] != NULL) free(ali_ref_seq[r_i]);
if(ali_ref_seq != NULL) free(ali_ref_seq);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_char[r_i] != NULL) free(read_char[r_i]);
if(read_char != NULL) free(read_char);
if(pos_ren[0][0] != NULL) free(pos_ren[0][0]);
if(pos_ren[0][1] != NULL) free(pos_ren[0][1]);
if(pos_ren[1][0] != NULL) free(pos_ren[1][0]);
if(pos_ren[1][1] != NULL) free(pos_ren[1][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(sub_mask1[r_i] != NULL) free(sub_mask1[r_i]);
if(sub_mask1 != NULL) free(sub_mask1);
for(r_i = 0; r_i < thread_n; r_i++)
if(sub_mask2[r_i] != NULL) free(sub_mask2[r_i]);
if(sub_mask2 != NULL) free(sub_mask2);
if(seedpos_misn[0][0] != NULL) free(seedpos_misn[0][0]);
if(seedpos_misn[0][1] != NULL) free(seedpos_misn[0][1]);
if(seedpos_misn[1][0] != NULL) free(seedpos_misn[1][0]);
if(seedpos_misn[1][1] != NULL) free(seedpos_misn[1][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(ex_d_mask1[r_i] != NULL) free(ex_d_mask1[r_i]);
if(ex_d_mask1 != NULL) free(ex_d_mask1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ex_d_mask2[r_i] != NULL) free(ex_d_mask2[r_i]);
if(ex_d_mask2 != NULL) free(ex_d_mask2);
#ifdef PAIR_RANDOM
for(r_i = 0; r_i < thread_n; r_i++)
if(b[r_i] != NULL) free(b[r_i]);
if(b != NULL) free(b);
for(r_i = 0; r_i < thread_n; r_i++)
if(ls[r_i] != NULL) free(ls[r_i]);
if(ls != NULL) free(ls);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_bit_pr[r_i] != NULL) free(read_bit_pr[r_i]);
if(read_bit_pr != NULL) free(read_bit_pr);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_val_pr[r_i] != NULL) free(read_val_pr[r_i]);
if(read_val_pr != NULL) free(read_val_pr);
for(r_i = 0; r_i < thread_n; r_i++)
if(kcol[r_i] != NULL) free(kcol[r_i]);
if(kcol != NULL) free(kcol);
if(seed_posn[0] != NULL) free(seed_posn[0]);
if(seed_posn[1] != NULL) free(seed_posn[1]);
if(seedn != NULL) free(seedn);
#endif
if(read_bit_1 != NULL) free(read_bit_1);
if(read_bit_2 != NULL) free(read_bit_2);
if(read_val_1 != NULL) free(read_val_1);
if(read_val_2 != NULL) free(read_val_2);
for(r_i = 0; r_i < thread_n; r_i++)
{
if(read_val1[r_i][0] != NULL) free(read_val1[r_i][0]);
if(read_val1[r_i][1] != NULL) free(read_val1[r_i][1]);
if(read_val1[r_i] != NULL) free(read_val1[r_i]);
}
if(read_val1 != NULL) free(read_val1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if(read_val2[r_i][0] != NULL) free(read_val2[r_i][0]);
if(read_val2[r_i][1] != NULL) free(read_val2[r_i][1]);
if(read_val2[r_i] != NULL) free(read_val2[r_i]);
}
if(read_val2 != NULL) free(read_val2);
#ifdef QUAL_FILT_LV
for(r_i = 0; r_i < thread_n; r_i++)
{
if(qual_filt_lv1[r_i][0] != NULL) free(qual_filt_lv1[r_i][0]);
if(qual_filt_lv1[r_i][1] != NULL) free(qual_filt_lv1[r_i][1]);
if(qual_filt_lv1[r_i] != NULL) free(qual_filt_lv1[r_i]);
}
if(qual_filt_lv1 != NULL) free(qual_filt_lv1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if(qual_filt_lv2[r_i][0] != NULL) free(qual_filt_lv2[r_i][0]);
if(qual_filt_lv2[r_i][1] != NULL) free(qual_filt_lv2[r_i][1]);
if(qual_filt_lv2[r_i] != NULL) free(qual_filt_lv2[r_i]);
}
if(qual_filt_lv2 != NULL) free(qual_filt_lv2);
#endif
#ifdef PR_COV_FILTER
if(cov_filt_f != NULL) free(cov_filt_f);
#endif
#endif
if(buffer_ref_seq != NULL) free(buffer_ref_seq);
if(buffer_seq != NULL) free(buffer_seq);
if(buffer_seqf != NULL) free(buffer_seqf);
//if(buffer_edge != NULL) free(buffer_edge);
if(buffer_p != NULL) free(buffer_p);
if(buffer_pp != NULL) free(buffer_pp);
if(buffer_hash_g != NULL) free(buffer_hash_g);
if(buffer_kmer_g != NULL) free(buffer_kmer_g);
if(buffer_off_g != NULL) free(buffer_off_g);
#ifdef KSW_ALN_PAIR
for(r_i = 0; r_i < thread_n; r_i++)
if(ali_ref_seq2[r_i] != NULL) free(ali_ref_seq2[r_i]);
if(ali_ref_seq2 != NULL) free(ali_ref_seq2);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_char2[r_i] != NULL) free(read_char2[r_i]);
if(read_char2 != NULL) free(read_char2);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_kl1[r_i] != NULL) free(op_dm_kl1[r_i]);
if(op_dm_kl1 != NULL) free(op_dm_kl1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_kr1[r_i] != NULL) free(op_dm_kr1[r_i]);
if(op_dm_kr1 != NULL) free(op_dm_kr1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_kl2[r_i] != NULL) free(op_dm_kl2[r_i]);
if(op_dm_kl2 != NULL) free(op_dm_kl2);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_kr2[r_i] != NULL) free(op_dm_kr2[r_i]);
if(op_dm_kr2 != NULL) free(op_dm_kr2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_kl1[r_i] != NULL) free(ops_dm_kl1[r_i]);
if(ops_dm_kl1 != NULL) free(ops_dm_kl1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_kr1[r_i] != NULL) free(ops_dm_kr1[r_i]);
if(ops_dm_kr1 != NULL) free(ops_dm_kr1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_kl2[r_i] != NULL) free(ops_dm_kl2[r_i]);
if(ops_dm_kl2 != NULL) free(ops_dm_kl2);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_kr2[r_i] != NULL) free(ops_dm_kr2[r_i]);
if(ops_dm_kr2 != NULL) free(ops_dm_kr2);
if(mat != NULL) free(mat);
#endif
#ifdef MAPPING_QUALITY
for(r_i = 0; r_i < thread_n; r_i++)
{
if(mp_subs1[r_i][0] != NULL) free(mp_subs1[r_i][0]);
if(mp_subs1[r_i][1] != NULL) free(mp_subs1[r_i][1]);
if(mp_subs1[r_i] != NULL) free(mp_subs1[r_i]);
}
if(mp_subs1 != NULL) free(mp_subs1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if(mp_subs2[r_i][0] != NULL) free(mp_subs2[r_i][0]);
if(mp_subs2[r_i][1] != NULL) free(mp_subs2[r_i][1]);
if(mp_subs2[r_i] != NULL) free(mp_subs2[r_i]);
}
if(mp_subs2 != NULL) free(mp_subs2);
if(sub_t != NULL) free(sub_t);
#endif
return 0;
}
#ifdef R_W_LOCK
int seed_ali_core(int read_seq_core, uint8_t tid)
#else
int seed_ali_core(uint32_t seqn, uint8_t tid)
#endif
{
uint8_t rc_i = 0;
uint8_t un_ii = 0;
uint8_t lv_ref_length_re1 = 0;
uint8_t lv_ref_length_re2 = 0;
uint8_t q_n1 = 0;
uint8_t q_n2 = 0;
uint8_t c_m_f = 0;
uint8_t end1_uc_f = 0;
uint8_t end2_uc_f = 0;
uint8_t nuc1_f = 0;
uint8_t nuc2_f = 0;
uint8_t b_t_n_r = 0;
uint8_t re_d = 0;
uint8_t single_lv_re = 0;
uint8_t rc_ii = 0;
uint8_t unmatch[2][2];
uint16_t max_mismatch = 0;
//uint8_t flow_f = 0;
char cigar_p1[MAX_LV_CIGARCOM];
char cigar_p2[MAX_LV_CIGARCOM];
uint16_t f_cigar[MAX_LV_CIGAR];
char sam_seq1[MAX_READLEN] = {};
char sam_seq2[MAX_READLEN] = {};
char cigarBuf1[MAX_LV_CIGAR] = {};
char cigarBuf2[MAX_LV_CIGAR] = {};
char str_o[MAX_LV_CIGAR];
char b_cigar[MAX_LV_CIGAR];
char* cp1 = NULL;
char* cp2 = NULL;
char* seq1p = NULL;
char* seq2p = NULL;
char* pch = NULL;
char* saveptr = NULL;
char* cigar_m_1 = NULL;
char* cigar_m_2 = NULL;
uint16_t ref_copy_num = 0;
uint16_t ref_copy_num1 = 0;
uint16_t ref_copy_num2 = 0;
uint16_t ref_copy_num_1 = 0;
uint16_t ref_copy_num_2 = 0;
uint16_t f_cigarn = 0;
uint16_t read_bit_char1 = 0;
uint16_t read_bit_char2 = 0;
int16_t rst_i = 0;
uint16_t s_m_t = 0;
uint16_t read_b_i = 0;
uint16_t f_c = 0;
uint16_t pchl = 0;
uint16_t f_i = 0;
uint16_t s_o = 0;
uint16_t snt = 0;
uint16_t d_n1 = 0;
uint16_t i_n1 = 0;
uint16_t no1_tmp = 0;
uint16_t no2_tmp = 0;
uint16_t read_length = 0;
uint16_t read_length1 = 0;
uint16_t read_length2 = 0;
uint16_t read_length_1 = 0;
uint16_t read_length_2 = 0;
uint16_t dm_i = 0;
uint32_t read_length_a1 = 0;
uint32_t read_length_a2 = 0;
uint32_t seqi = 0;
uint32_t v_cnt = 0;
uint32_t vs_cnt = 0;
uint32_t ref_copy_num_chars = 0;
uint32_t ref_copy_num_chars1 = 0;
uint32_t ref_copy_num_chars2 = 0;
uint32_t ref_copy_num_chars_1 = 0;
uint32_t ref_copy_num_chars_2 = 0;
uint32_t r_i = 0;
uint32_t psp_i = 0;
uint32_t d_l1 = 0;
uint32_t d_l2 = 0;
uint32_t d_r1 = 0;
uint32_t d_r2 = 0;
uint32_t mis_c_n = 0;
uint32_t mis_c_n_filt = 0;
uint32_t xa_i = 0;
uint32_t xa_i_1 = 0;
uint32_t xa_i_2 = 0;
uint32_t v_cnt_i = 0;
uint32_t va_cnt_i = 0;
uint32_t sam_flag1 = 0;
uint32_t sam_flag2 = 0;
uint32_t seed1_i = 0;
uint32_t seed2_i = 0;
uint32_t sam_seq_i = 0;
uint32_t rc_f = 0;
uint32_t max_pair_score = 0;
uint32_t seed_posn_filter = 0;
#ifdef QUALS_CHECK
uint8_t error_f = 0;
#endif
int dm_op_p = 0;
int s_r_o_l1 = 0;
int s_r_o_r1 = 0;
int s_r_o_l2 = 0;
int s_r_o_r2 = 0;
int lv_re1f = 0;
int lv_re1b = 0;
int lv_re2f = 0;
int lv_re2b = 0;
int chr_re = 0;
int chr_re1 = 0;
int chr_re2 = 0;
int mid = 0;
int low = 0;
int high = 0;
int m_m_n = 0;
int sn = 0;
int dm12 = 0;
int dm1 = 0;
int dm2 = 0;
int dm_l1 = 0;
int dm_r1 = 0;
int dm_l2 = 0;
int dm_r2 = 0;
int dmt1 = 0;
int dmt2 = 0;
int lv_dmt1 = 0;
int lv_dmt2 = 0;
int ld1 = 0;
int rd1 = 0;
int ld2 = 0;
int rd2 = 0;
int ksw_re = 0;
int cmp_re = 0;
int q_rear_i = 0;
int q_rear1 = 0;
int q_rear2 = 0;
int cache_dml1[MAX_Q_NUM];
int cache_dml2[MAX_Q_NUM];
int cache_dmr1[MAX_Q_NUM];
int cache_dmr2[MAX_Q_NUM];
int cache_dis1[MAX_Q_NUM];
int cache_dis2[MAX_Q_NUM];
int cache_kl1[MAX_Q_NUM];
int cache_kr1[MAX_Q_NUM];
int cache_kl2[MAX_Q_NUM];
int cache_kr2[MAX_Q_NUM];
int nm_score1 = 0;
int nm_score2 = 0;
uint32_t spa_i[2][2];
uint64_t c_tmp = 0;
uint64_t xor_tmp = 0;
uint64_t ref_tmp_ori = 0;
uint64_t ref_tmp_ori2 = 0;
uint64_t tran_tmp_p = 0;
uint64_t tran_tmp = 0;
int64_t sam_cross = 0;
int64_t sam_pos1 = 0;
int64_t sam_pos2 = 0;
uint64_t cache_end1[MAX_Q_NUM][MAX_REF_SEQ_C];
uint64_t cache_end2[MAX_Q_NUM][MAX_REF_SEQ_C];
uint64_t low_mask = 0;
uint16_t* sub_mask = NULL;
uint64_t* ex_d_mask = NULL;
#ifdef SEED_FILTER_LENGTH
uint16_t seed_no[2][2];
uint16_t max_read_length[2][2];
uint16_t max_sets_n[2][2];
uint16_t off_i = 0;
#endif
int64_t bit_char_i = 0;
int64_t bit_char_i_ref = 0;
cnt_re cnt;
#ifdef ANCHOR_HASH_ALI
uint8_t ori_i = 0;
uint16_t tra_i;
uint8_t base_re = 0;
uint8_t anchor_hash_i = 0;
uint16_t des_i = 0;
uint16_t print_i;
uint16_t array_index;
uint16_t char_i = 0;
uint16_t buffer_i = 0;
uint16_t seed_length = 0;
uint16_t max_seed_length = 0;
uint16_t lv_k = 0;
uint16_t lv_k1 = 0;
uint16_t lv_k2 = 0;
uint16_t lv_k_1 = 0;
uint16_t lv_k_2 = 0;
uint32_t read_k_p = 0;
uint32_t read_k_t = 0;
uint32_t anchor_mask = 0;
uint32_t array_i = 0;
uint32_t array_i_p = 0;
uint32_t anchor_ref = 0;
uint32_t r_b_v = 0;
uint32_t max_right = 0;
int left_i = 0;
int right_i = 0;
uint64_t* ori = NULL;
anchor_mask = ((uint32_t )1 << k_anchor_b) - 1;
uint16_t* anchor_hash_p = NULL;
uint8_t* anchor_array_p = NULL;
uint16_t* anchor_point_p = NULL;
uint16_t* anchor_pos_p = NULL;
#endif
seed_pa* seed_pr1 = NULL;
seed_pa* seed_pr2 = NULL;
seed_pa* seed_pr[2][2];
seed_pr[0][0] = NULL;
seed_pr[0][1] = NULL;
seed_pr[1][0] = NULL;
seed_pr[1][1] = NULL;
//for # position
int16_t pound_pos1_f_forward = 0;
int16_t pound_pos1_f_reverse = 0;
int16_t pound_pos1_r_forward = 0;
int16_t pound_pos1_r_reverse = 0;
int16_t pound_pos2_f_forward = 0;
int16_t pound_pos2_f_reverse = 0;
int16_t pound_pos2_r_forward = 0;
int16_t pound_pos2_r_reverse = 0;
int16_t pound_mis = 0;
int16_t pound_pos_1_f = 0;
int16_t pound_pos_1_r = 0;
int16_t pound_pos_2_f = 0;
int16_t pound_pos_2_r = 0;
int16_t lv_up_left = 0;
int16_t lv_up_right = 0;
int16_t lv_down_right = 0;
int16_t lv_down_left = 0;
int16_t dm_cir_1 = 0;
int16_t dm_cir_2 = 0;
int16_t dm_cir = 0;
int16_t dm_cir_min = 0;
int16_t cache_dm_cir1[MAX_Q_NUM];
int16_t cache_dm_cir2[MAX_Q_NUM];
int16_t read_pos_re = 0;
int16_t read_pos_end_re = 0;
int16_t read_pos_start_num = 0;
int16_t read_pos_end_num = 0;
int16_t rst_i_1 = 0;
int16_t m_n_f = 0;
int16_t m_n_b = 0;
int16_t s_r_o_l = 0;
int16_t s_r_o_r = 0;
uint8_t cir_n = 0;
#ifdef KSW_ALN_PAIR
int band_with = 33;//100
int zdrop = 0;//100
int end_bonus = 5;
int tle;
int gtle;
int gscore;
int max_off;
#endif
#ifdef QUAL_FILT
uint64_t* qual_filt_1 = NULL;
uint64_t* qual_filt_2 = NULL;
uint8_t qual_filt_fix = 55;
#endif
#ifdef QUAL_FILT_LV
uint8_t* qual_filt_lv_1 = NULL;
uint8_t* qual_filt_lv_2 = NULL;
uint8_t* qual_filt_lv_1_o = NULL;
uint8_t* qual_filt_lv_2_o = NULL;
uint16_t mis_n1 = 0;
uint16_t mis_n2 = 0;
#endif
uint16_t s_offset1 = 0;
uint16_t s_offset2 = 0;
#ifdef ALTER_DEBUG
uint16_t seed_length1 = 0;
uint16_t seed_length2 = 0;
#endif
#ifdef MAPPING_QUALITY
float m_sub_tmp = 0;
#endif
#ifdef UNPIPATH_OFF_K20
uint64_t pos_l = 0;
uint64_t posi = 0;
uint64_t x = 0;
uint64_t ksw_s = 0;
uint64_t ksw_e = 0;
uint64_t base_i = 0;
uint64_t base_i_off_l = 0;
uint64_t base_i_off_r = 0;
#else
uint32_t pos_l = 0;
uint32_t posi = 0;
uint32_t x = 0;
uint32_t ksw_s = 0;
uint32_t ksw_e = 0;
uint32_t base_i = 0;
uint32_t base_i_off_l = 0;
uint32_t base_i_off_r = 0;
#endif
uint64_t low_mask_1 = 0;
uint64_t low_mask_2 = 0;
#ifdef READN_RANDOM_SEED
char tmp_char;
uint16_t readn_re1 = 0;
uint16_t readn_re2 = 0;
#endif
#ifdef CIGAR_LEN_ERR
int cigar_len = 0;
int cigar_len_tmp = 0;
int cigar_len_re = 0;
uint16_t pchl_tmp = 0;
uint16_t s_o_tmp = 0;
char* pch_tmp = NULL;
char* saveptr_tmp = NULL;
char cigar_tmp[MAX_LV_CIGARCOM];
#endif
uint8_t qual_flag = 0;
#ifdef REDUCE_ANCHOR
int ls = 0;
int rs = 0;
uint8_t rcs = 0;
uint16_t tra1_i = 0;
uint16_t tra2_i = 0;
uint16_t anchor_n1 = 0;
uint16_t anchor_n2 = 0;
uint8_t other_end_flag = 0;
uint16_t op_mask[MAX_REDUCE_ANCHOR_NUM];
uint16_t ops_mask[MAX_REDUCE_ANCHOR_NUM];
#endif
#ifdef ANCHOR_LV_S
int16_t s_offset_l = 0;
int16_t s_offset_r = 0;
#endif
uint64_t* op_vector_seq1_tmp = NULL;
uint16_t v_cnt_i_tmp = 0;
#ifdef FIX_SV
uint16_t tra_i_n = 0;
uint8_t sv_add = 0;
#endif
#ifdef FIX_SA
uint8_t op_rc_tmp = 0;
uint16_t sv_s_len = 0;
uint16_t sv_s_len_p = 0;
#endif
#ifndef R_W_LOCK
for(seqi = 0; seqi < seqn; seqi++)
#else
if(1)
#endif
{
#ifndef R_W_LOCK
#ifdef PTHREAD_USE
if ((seqi % thread_n) != tid) continue;
#endif
#else
seqi = read_seq_core;
#endif
read_length1 = seqio[seqi].read_length1;
read_length2 = seqio[seqi].read_length2;
lv_k1 = (read_length1 * lv_rate) + 1;
lv_k2 = (read_length2 * lv_rate) + 1;
if((insert_dis < read_length1) || (insert_dis < read_length2))
{
fprintf(stderr, "Input error: wrong -u or -f\n");
exit(1);
}
end_dis1[tid] = insert_dis - read_length2;
end_dis2[tid] = insert_dis - read_length1;
read_length_a1 = read_length1 - 1;
read_length_a2 = read_length2 - 1;
f_cigarn = (read_length1 > read_length2) ? read_length1: read_length2;
f_cigar[f_cigarn] = '\0';
//sprintf(cigar_m1[tid],"%uM\0",read_length1);
//sprintf(cigar_m2[tid],"%uM\0",read_length2);
sprintf(cigar_m1[tid],"%uM",read_length1);
sprintf(cigar_m2[tid],"%uM",read_length2);
//for bit operation
read_bit_char1 = (((uint16_t )((read_length_a1 >> 5) + 1)) << 3);
read_bit_char2 = (((uint16_t )((read_length_a2 >> 5) + 1)) << 3);
ref_copy_num1 = ((read_length_a1) >> 5) + 3;
ref_copy_num_chars1 = (ref_copy_num1 << 3);
lv_ref_length_re1 = (read_length1 & 0X1f);
for(r_i = 0; r_i <= 32 - lv_ref_length_re1; r_i++)
{
ex_d_mask1[tid][r_i] = bit_assi[lv_ref_length_re1 + r_i];
sub_mask1[tid][r_i] = ref_copy_num1 - 2;
}
for(r_i = 33 - lv_ref_length_re1; r_i <= 32; r_i++)
{
ex_d_mask1[tid][r_i] = bit_assi[lv_ref_length_re1 + r_i - 32];
sub_mask1[tid][r_i] = ref_copy_num1 - 1;
}
low_mask1[tid] = bit_assi[lv_ref_length_re1];
//for bit operation
ref_copy_num2 = ((read_length_a2) >> 5) + 3;
ref_copy_num_chars2 = (ref_copy_num2 << 3);
lv_ref_length_re2 = (read_length2 & 0X1f);
for(r_i = 0; r_i <= 32 - lv_ref_length_re2; r_i++)
{
ex_d_mask2[tid][r_i] = bit_assi[lv_ref_length_re2 + r_i];
sub_mask2[tid][r_i] = ref_copy_num2 - 2;
}
for(r_i = 33 - lv_ref_length_re2; r_i <= 32; r_i++)
{
ex_d_mask2[tid][r_i] = bit_assi[lv_ref_length_re2 + r_i - 32];
sub_mask2[tid][r_i] = ref_copy_num2 - 1;
}
low_mask2[tid] = bit_assi[lv_ref_length_re2];
max_pair_score = (uint32_t )(((float )(read_length1 + read_length2)) * max_pair_score_r);
cov_a_n[tid][0] = ((read_length_a1) >> 6) + 1;//2
cov_a_n[tid][1] = ((read_length_a2) >> 6) + 1;
max_mismatch1[tid] = (uint16_t )(((float )read_length1) * mis_match_r);
max_mismatch2[tid] = (uint16_t )(((float )read_length2) * mis_match_r);
max_mismatch1_single[tid] = (uint16_t )(((float )read_length1) * mis_match_r_single);
max_mismatch2_single[tid] = (uint16_t )(((float )read_length2) * mis_match_r_single);
memset(read_bit1[tid][0], 0, read_bit_char1);
memset(read_bit1[tid][1], 0, read_bit_char1);
memset(read_bit2[tid][0], 0, read_bit_char2);
memset(read_bit2[tid][1], 0, read_bit_char2);
r_i = 0;
while ((seqio[seqi].read_seq1)[r_i])
{
#ifdef READN_RANDOM_SEED
tmp_char = (seqio[seqi].read_seq1)[r_i];
if(tmp_char == 'N')
{
readn_re1 = readn_cnt & 0X3ff;
readn_re2 = readn_cnt & 0Xf;
c_tmp = ((random_buffer_readn[readn_re1] >> (readn_re2 << 1)) & 0X3);
readn_cnt++;
}
else c_tmp = charToDna5n[tmp_char];
#else
c_tmp = charToDna5n[(seqio[seqi].read_seq1)[r_i]];
#endif
#ifdef ALI_LV
read_val1[tid][0][r_i] = c_tmp;
read_val1[tid][1][read_length_a1 - r_i] = c_tmp ^ 0X3;
#endif
read_bit1[tid][0][r_i >> 5] |= (((uint64_t )c_tmp) << ((31 - (r_i & 0X1f)) << 1));
read_bit1[tid][1][(read_length_a1 - r_i) >> 5] |= (((uint64_t )(c_tmp ^ 0X3)) << ((31 - ((read_length_a1 - r_i) & 0X1f)) << 1));
r_i++;
}
r_i = 0;
while ((seqio[seqi].read_seq2)[r_i])
{
#ifdef READN_RANDOM_SEED
tmp_char = (seqio[seqi].read_seq2)[r_i];
if(tmp_char == 'N')
{
readn_re1 = readn_cnt & 0X3ff;
readn_re2 = readn_cnt & 0Xf;
c_tmp = ((random_buffer_readn[readn_re1] >> (readn_re2 << 1)) & 0X3);
readn_cnt++;
}
else c_tmp = charToDna5n[tmp_char];
#else
c_tmp = charToDna5n[(seqio[seqi].read_seq2)[r_i]];
#endif
#ifdef ALI_LV
read_val2[tid][0][r_i] = c_tmp;
read_val2[tid][1][read_length_a2 - r_i] = c_tmp ^ 0X3;
#endif
read_bit2[tid][0][r_i >> 5] |= (((uint64_t )c_tmp) << ((31 - (r_i & 0X1f)) << 1));
read_bit2[tid][1][(read_length_a2 - r_i) >> 5] |= (((uint64_t )(c_tmp ^ 0X3)) << ((31 - ((read_length_a2 - r_i) & 0X1f)) << 1));
r_i++;
}
#ifdef QUAL_FILT
memset(qual_filt1[tid][0], 0, read_bit_char1);
memset(qual_filt1[tid][1], 0, read_bit_char1);
memset(qual_filt2[tid][0], 0, read_bit_char2);
memset(qual_filt2[tid][1], 0, read_bit_char2);
c_tmp = 3;
for(r_i = 0; r_i < read_length1; r_i++)
{
if(seqio[seqi].qual1[r_i] < qual_filt_fix) //'7': 55 63
{
qual_filt1[tid][0][r_i >> 5] |= (((uint64_t )c_tmp) << ((31 - (r_i & 0X1f)) << 1));
qual_filt1[tid][1][(read_length_a1 - r_i) >> 5] |= (((uint64_t )c_tmp) << ((31 - ((read_length_a1 - r_i) & 0X1f)) << 1));
}
}
for(r_i = 0; r_i < read_length2; r_i++)
{
if(seqio[seqi].qual2[r_i] < qual_filt_fix) //'7': 55 63
{
qual_filt2[tid][0][r_i >> 5] |= (((uint64_t )c_tmp) << ((31 - (r_i & 0X1f)) << 1));
qual_filt2[tid][1][(read_length_a2 - r_i) >> 5] |= (((uint64_t )c_tmp) << ((31 - ((read_length_a2 - r_i) & 0X1f)) << 1));
}
}
for(r_i = 0; r_i < (read_length1 >> 5) + 1; r_i++)
qual_filt1[tid][0][r_i] = ~qual_filt1[tid][0][r_i];
for(r_i = 0; r_i < (read_length1 >> 5) + 1; r_i++)
qual_filt1[tid][1][r_i] = ~qual_filt1[tid][1][r_i];
for(r_i = 0; r_i < (read_length2 >> 5) + 1; r_i++)
qual_filt2[tid][0][r_i] = ~qual_filt2[tid][0][r_i];
for(r_i = 0; r_i < (read_length2 >> 5) + 1; r_i++)
qual_filt2[tid][1][r_i] = ~qual_filt2[tid][1][r_i];
#ifdef QUAL_FILT_LV
for(r_i = 0; r_i < read_length1; r_i++)
{
if(seqio[seqi].qual1[r_i] < qual_filt_fix) qual_filt_lv1[tid][0][r_i] = 0;
else qual_filt_lv1[tid][0][r_i] = 3;
}
for(r_i = 0; r_i < read_length1; r_i++)
{
if(seqio[seqi].qual1[r_i] < qual_filt_fix) qual_filt_lv1[tid][1][read_length_a1 - r_i] = 0;
else qual_filt_lv1[tid][1][read_length_a1 - r_i] = 3;
}
for(r_i = 0; r_i < read_length2; r_i++)
{
if(seqio[seqi].qual2[r_i] < qual_filt_fix) qual_filt_lv2[tid][0][r_i] = 0;
else qual_filt_lv2[tid][0][r_i] = 3;
}
for(r_i = 0; r_i < read_length2; r_i++)
{
if(seqio[seqi].qual2[r_i] < qual_filt_fix) qual_filt_lv2[tid][1][read_length_a2 - r_i] = 0;
else qual_filt_lv2[tid][1][read_length_a2 - r_i] = 3;
}
#endif
#endif
#ifdef MAPPING_QUALITY
for(r_i = 0; r_i < read_length1; r_i++)
{
m_sub_tmp = mp_sub_bp[seqio[seqi].qual1[r_i]];
mp_subs1[tid][0][r_i] = m_sub_tmp;
mp_subs1[tid][1][read_length_a1 - r_i] = m_sub_tmp;
}
for(r_i = 0; r_i < read_length2; r_i++)
{
m_sub_tmp = mp_sub_bp[seqio[seqi].qual2[r_i]];
mp_subs2[tid][0][r_i] = m_sub_tmp;
mp_subs2[tid][1][read_length_a2 - r_i] = m_sub_tmp;
}
#endif
pound_pos1_f_forward = read_length1;
pound_pos1_r_forward = read_length1;
pound_pos1_f_reverse = 0;
pound_pos1_r_reverse = 0;
pound_pos2_f_forward = read_length2;
pound_pos2_r_forward = read_length2;
pound_pos2_f_reverse = 0;
pound_pos2_r_reverse = 0;
for(r_i = 0; r_i < read_length1; r_i++)
if(seqio[seqi].qual1[r_i] == '#')
{
pound_pos1_f_forward = r_i;
pound_pos1_r_reverse = read_length1 - r_i;
break;
}
for(r_i = 0; r_i < read_length2; r_i++)
if(seqio[seqi].qual2[r_i] == '#')
{
pound_pos2_f_forward = r_i;
pound_pos2_r_reverse = read_length2 - r_i;
break;
}
de_m_p[tid] = 1;
de_m_p_o[tid] = 1;
seed_l[tid] = seed_l_max;
#ifdef PAIR_SEED_LENGTH_FILT
max_lengtht[tid] = 0;
#endif
rc_f = 0;
#ifdef PR_COV_FILTER
cov_filt_f[tid] = 0;
#endif
#ifdef PR_SINGLE
seed_re_r[tid] = 0;
#endif
#ifdef TER_J
dm_op_p = 0;
v_cnt_p = 0;
#endif
dm_op_p = MAX_OP_SCORE;
#ifdef ALTER_DEBUG
rep_go[tid] = 1;
#endif
cir_n = 1;
while(cir_n <= cir_fix_n)
{
dm_op[tid] = MAX_OP_SCORE;
dm_ops[tid] = MAX_OP_SCORE;
v_cnt = 0;
vs_cnt = 0;
mat_posi[tid] = 0;
rc_f = 0Xffffffff;
dm_cir_min = 0Xfff;
unmatch[0][0] = 0;
unmatch[0][1] = 0;
unmatch[1][0] = 0;
unmatch[1][1] = 0;
#ifdef PAIR_RANDOM
if(cir_n == 1)
{
pos_ren[0][0][tid] = 0;
pos_ren[0][1][tid] = 0;
pos_ren[1][0][tid] = 0;
pos_ren[1][1][tid] = 0;
}
#endif
for(rc_i = 0; rc_i < 2; rc_i++)
{
rc_cov_f[tid] = 0;
#ifdef SEED_FILTER_LENGTH
max_read_length[rc_i][rc_i] = 0;
#ifdef UNPIPATH_OFF_K20
if((seed_pr[rc_i][rc_i] = single_seed_reduction_core_filter64(seedpa1[rc_i][tid], read_bit1[tid][rc_i], read_val1[tid][rc_i], &(spa_i[rc_i][rc_i]), &(seed_set_pos[rc_i][rc_i][tid]), &(pos_ren[rc_i][rc_i][tid]), tid, read_length1, &(seed_no[rc_i][rc_i]), &(max_read_length[rc_i][rc_i]))) == NULL)
#else
if((seed_pr[rc_i][rc_i] = single_seed_reduction_core_filter(seedpa1[rc_i][tid], read_bit1[tid][rc_i], read_val1[tid][rc_i], &(spa_i[rc_i][rc_i]), &(seed_set_pos[rc_i][rc_i][tid]), &(pos_ren[rc_i][rc_i][tid]), tid, read_length1, &(seed_no[rc_i][rc_i]), &(max_read_length[rc_i][rc_i]))) == NULL)
#endif
#else
if((seed_pr[rc_i][rc_i] = single_seed_reduction_core(seedpa1[rc_i][tid], read_bit1[tid][rc_i], read_val1[tid][rc_i], &(spa_i[rc_i][rc_i]), &(seed_set_pos[rc_i][rc_i][tid]), &(pos_ren[rc_i][rc_i][tid]), tid, read_length1)) == NULL)
#endif
{
#ifdef UNMATCH_SINGLE_END
unmatch[rc_i][rc_i] = 1;
#endif
#ifdef UNMATCH_SINGLE_END_MIS
unmatch[rc_i][rc_i] = 1;
#endif
}
rc_cov_f[tid] = 1;
#ifdef SEED_FILTER_LENGTH
max_read_length[rc_i][1 - rc_i] = 0;
#ifdef UNPIPATH_OFF_K20
if((seed_pr[rc_i][1 - rc_i] = single_seed_reduction_core_filter64(seedpa2[rc_i][tid], read_bit2[tid][1 - rc_i], read_val2[tid][1 - rc_i], &(spa_i[rc_i][1 - rc_i]), &(seed_set_pos[rc_i][1 - rc_i][tid]), &(pos_ren[rc_i][1 - rc_i][tid]), tid, read_length2, &(seed_no[rc_i][1 - rc_i]), &(max_read_length[rc_i][1 - rc_i]))) == NULL)
#else
if((seed_pr[rc_i][1 - rc_i] = single_seed_reduction_core_filter(seedpa2[rc_i][tid], read_bit2[tid][1 - rc_i], read_val2[tid][1 - rc_i], &(spa_i[rc_i][1 - rc_i]), &(seed_set_pos[rc_i][1 - rc_i][tid]), &(pos_ren[rc_i][1 - rc_i][tid]), tid, read_length2, &(seed_no[rc_i][1 - rc_i]), &(max_read_length[rc_i][1 - rc_i]))) == NULL)
#endif
#else
if((seed_pr[rc_i][1 - rc_i] = single_seed_reduction_core(seedpa2[rc_i][tid], read_bit2[tid][1 - rc_i], read_val2[tid][1 - rc_i], &(spa_i[rc_i][1 - rc_i]), &(seed_set_pos[rc_i][1 - rc_i][tid]), &(pos_ren[rc_i][1 - rc_i][tid]), tid, read_length2)) == NULL)
#endif
{
#ifdef UNMATCH_SINGLE_END
unmatch[rc_i][1 - rc_i] = 1;
#endif
#ifdef UNMATCH_SINGLE_END_MIS
unmatch[rc_i][1 - rc_i] = 1;
#endif
}
if((seed_pr[rc_i][rc_i] != NULL) && (seed_pr[rc_i][1 - rc_i] != NULL))
{
#ifdef UNPIPATH_OFF_K20
merge_pair_end64(spa_i[rc_i][0], spa_i[rc_i][1], seed_pr[rc_i][0], seed_pr[rc_i][1], seed_set_pos[rc_i][0][tid], seed_set_pos[rc_i][1][tid], rc_i, tid);
#else
merge_pair_end(spa_i[rc_i][0], spa_i[rc_i][1], seed_pr[rc_i][0], seed_pr[rc_i][1], seed_set_pos[rc_i][0][tid], seed_set_pos[rc_i][1][tid], rc_i, tid);
#endif
if(rc_i == 0) rc_f = mat_posi[tid];
}
}
if(de_m_p[tid] == 1)
{
seed_l[tid] -= seed_step;
}
else
{
no1_tmp = 0Xffff;
no2_tmp = 0Xffff;
for(r_i = 0; r_i < mat_posi[tid]; r_i++)
{
seed1_i = seed_no1[tid][r_i];
seed2_i = seed_no2[tid][r_i];
if(mat_rc[tid][r_i] == 0)
{
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
read_val_1[tid] = read_val1[tid][0];
read_val_2[tid] = read_val2[tid][1];
#ifdef QUAL_FILT
qual_filt_1 = qual_filt1[tid][0];
qual_filt_2 = qual_filt2[tid][1];
#endif
#ifdef QUAL_FILT_LV
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_2 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
qual_filt_lv_2_o = qual_filt_lv2[tid][0];
#endif
seed_pr1 = seed_pr[0][0];
seed_pr2 = seed_pr[0][1];
read_length_1 = read_length1;
read_length_2 = read_length2;
ref_copy_num_1 = ref_copy_num1;
ref_copy_num_2 = ref_copy_num2;
ref_copy_num_chars_1 = ref_copy_num_chars1;
ref_copy_num_chars_2 = ref_copy_num_chars2;
low_mask_1 = low_mask1[tid];
low_mask_2 = low_mask2[tid];
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
if(mat_rc[tid][r_i] == 1)
{
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
read_val_1[tid] = read_val2[tid][0];
read_val_2[tid] = read_val1[tid][1];
#ifdef QUAL_FILT
qual_filt_1 = qual_filt2[tid][0];
qual_filt_2 = qual_filt1[tid][1];
#endif
#ifdef QUAL_FILT_LV
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_2 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
qual_filt_lv_2_o = qual_filt_lv1[tid][0];
#endif
seed_pr1 = seed_pr[1][0];
seed_pr2 = seed_pr[1][1];
read_length_1 = read_length2;
read_length_2 = read_length1;
ref_copy_num_1 = ref_copy_num2;
ref_copy_num_2 = ref_copy_num1;
ref_copy_num_chars_1 = ref_copy_num_chars2;
ref_copy_num_chars_2 = ref_copy_num_chars1;
low_mask_1 = low_mask2[tid];
low_mask_2 = low_mask1[tid];
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
#ifdef PAIR_SEED_LENGTH_FILT
if(seed_pr1[seed1_i].length + seed_pr2[seed2_i].length < max_lengtht[tid] - length_reducet) continue;
#endif
if(r_i == rc_f)
{
no1_tmp = 0Xffff;
no2_tmp = 0Xffff;
}
if(seed1_i != no1_tmp)
{
//current seed does not cross one unipath
if(seed_pr1[seed1_i].ui == 1)
{
end1_uc_f = 0;
nuc1_f = 0;
d_l1 = seed_pr1[seed1_i].ref_pos_off;
d_r1 = seed_pr1[seed1_i].ref_pos_off_r;
}
else
{
end1_uc_f = 1;
}
q_rear1 = 0;
q_n1 = 0;
dmt1 = ali_exl;
lv_dmt1 = lv_k1;
s_r_o_l1 = seed_pr1[seed1_i].s_r_o_l;
s_r_o_r1 = seed_pr1[seed1_i].s_r_o_r;
#ifdef ALTER_DEBUG
seed_length1 = seed_pr1[seed1_i].length;
#endif
no1_tmp = seed1_i;
}
if(seed2_i != no2_tmp)
{
//current seed does not cross one unipath
if(seed_pr2[seed2_i].ui == 1)
{
end2_uc_f = 0;
nuc2_f = 0;
d_l2 = seed_pr2[seed2_i].ref_pos_off;
d_r2 = seed_pr2[seed2_i].ref_pos_off_r;
}
else
{
end2_uc_f = 1;
}
q_rear2 = 0;
q_n2 = 0;
dmt2 = ali_exl;
lv_dmt2 = lv_k2;
s_r_o_l2 = seed_pr2[seed2_i].s_r_o_l;
s_r_o_r2 = seed_pr2[seed2_i].s_r_o_r;
#ifdef ALTER_DEBUG
seed_length2 = seed_pr2[seed2_i].length;
#endif
no2_tmp = seed2_i;
}
#ifdef ALI_B_V_R
//alignment
//for end1
if((end1_uc_f == 0) && ((dmt1 <= d_l1) && (dmt1 <= d_r1))) // && (nuc1_f == 0)
{
if(nuc1_f == 0)
{
//lv_f1 = 0;
pos_l = mat_pos1[tid][r_i] - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars_1);
for(rst_i = 0; rst_i < ref_copy_num_1 - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask_1;
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars_1);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num_1 - 1] &= low_mask_1;
}
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num_1 - 2];
ref_seq_tmp1[tid][ref_copy_num_1 - 2] &= low_mask_1;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num_1 - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch1[tid]) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch1[tid]) break;
#endif
}
ref_seq_tmp1[tid][ref_copy_num_1 - 2] = ref_tmp_ori;
if(mis_c_n_filt > max_mismatch1[tid])
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(s_r_o_l1 + 1, read_char[tid], 33 + s_r_o_l1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_l1, &tle, >le, &gscore, &max_off);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length_1; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length_1 + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(read_length_1 - s_r_o_r1, read_char[tid], 32 + read_length_1 - s_r_o_r1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_r1, &tle, >le, &gscore, &max_off);
dm1 = MAX_OP_SCORE_P1 - (dm_l1 + dm_r1); //read length cannot be more than 1024
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
#ifdef SPLIT_LV
pound_mis = 0;
if(pound_pos_1_f >= s_r_o_r1) //1
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f < pound_pos_1_r)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r1;
}
else if(pound_pos_1_r <= s_r_o_l1 + 1) //5
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_r > 0)
{
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r1;
}
else if((pound_pos_1_f <= s_r_o_l1 + 1) && (pound_pos_1_r >= s_r_o_r1)) //2
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i <= s_r_o_l1) && (bit_char_i_ref <= s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f <= s_r_o_l1)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = s_r_o_l1 >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = (s_r_o_l1 & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
}
else if((pound_pos_1_f > s_r_o_l1 + 1) && (pound_pos_1_f < s_r_o_r1)) //3
{
#ifdef POUND_MIS
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
}
else //4
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < s_r_o_l1) && (bit_char_i_ref < s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_l1 > 0)
{
read_pos_end_num = (s_r_o_l1 - 1) >> 5;
read_pos_end_re = ((s_r_o_l1 - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
#ifdef POUND_MODIFY
lv_down_left = s_r_o_r1;
#else
lv_down_left = s_r_o_l1;
#endif
}
#ifdef QUAL_FILT_LV
#ifdef QUAL_FILT_LV_MIS
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#ifdef S_DEBUG
printf("extension lv1 %u: %u %d %d\n", mat_rc[tid][r_i], lv_dmt1, lv_up_right, lv_up_left);
#endif
dm_l1 = computeEditDistance_mis(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length_a1 - lv_up_right);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], qual_filt_lv_1 + lv_down_left);
dm1 = dm_l1 + dm_r1 + pound_mis;
dm_cir_1 = dm_l1 + dm_r1;// + pound_mis
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance_misboth(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], L_mis[tid], qual_filt_lv_1_o + read_length_a1 - lv_up_right, &mis_n1);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance_misboth(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], L_mis[tid], qual_filt_lv_1 + lv_down_left, &mis_n2);
dm1 = mis_n1 + mis_n2 + pound_mis;
dm_cir_1 = dm_l1 + dm_r1;// + pound_mis
#endif
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#else
#ifdef LAST_CIRCLE_NOPOUND
pound_mis = 0;
#endif
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid]);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid]);
dm1 = dm_l1 + dm_r1 + pound_mis;
dm_cir_1 = dm_l1 + dm_r1;// + pound_mis
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
#endif
}
}
else
{
dm1 = mis_c_n;
dm_cir_1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1))
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch1[tid] - 1) dmt1 = 0;
}
else
{
dm1 = MAX_EDIT_SCORE;
dm_cir_1 = MAX_EDIT_SCORE;
}
nuc1_f = 1;
}
}
else
{
pos_l = mat_pos1[tid][r_i] - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars_1);
for(rst_i = 0; rst_i < ref_copy_num_1 - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask_1;
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars_1);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num_1 - 1] &= low_mask_1;
}
//trim the beginning and end of the current ref seq based on current minimum edit distance dm_t
s_m_t = sub_mask1[tid][dmt1];
ref_seq_tmp1[tid][0] &= bit_tran[dmt1];
ref_seq_tmp1[tid][s_m_t] &= ex_d_mask1[tid][dmt1];
//traverse and check whether there is an existing seq that is as same as current new ref seq
c_m_f = 0;
for(q_rear_i = q_rear1 - 1; q_rear_i >= 0; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask1[tid][dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
//lv_f1 = cache_lvf1[q_rear_i];
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
dm_cir_1 = cache_dm_cir1[q_rear_i];
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
dm_l1 = cache_kl1[q_rear_i];
dm_r1 = cache_kr1[q_rear_i];
}
#endif
c_m_f = 1;
break;
}
}
if((q_n1 > MAX_Q_NUM) && (q_rear_i < 0))
{
for(q_rear_i = MAX_Q_NUM - 1; q_rear_i >= q_rear1; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask1[tid][dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
//lv_f1 = cache_lvf1[q_rear_i];
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
dm_cir_1 = cache_dm_cir1[q_rear_i];
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
dm_l1 = cache_kl1[q_rear_i];
dm_r1 = cache_kr1[q_rear_i];
}
#endif
c_m_f = 1;
break;
}
}
}
//do not find the seq in cache, exact match or lv and add into cache
if(c_m_f == 0)
{
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num_1 - 2];
ref_seq_tmp1[tid][ref_copy_num_1 - 2] &= low_mask_1;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num_1 - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch1[tid]) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch1[tid]) break;
#endif
//mis_c_n += popcount_3(ref_seq_tmp1[rst_i] ^ read_bit_1[read_b_i]);
}
ref_seq_tmp1[tid][ref_copy_num_1 - 2] = ref_tmp_ori;
//lv
if(mis_c_n_filt > max_mismatch1[tid])
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(s_r_o_l1 + 1, read_char[tid], 33 + s_r_o_l1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_l1, &tle, >le, &gscore, &max_off);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length_1; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length_1 + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(read_length_1 - s_r_o_r1, read_char[tid], 32 + read_length_1 - s_r_o_r1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_r1, &tle, >le, &gscore, &max_off);
dm1 = MAX_OP_SCORE_P1 - (dm_l1 + dm_r1); //read length cannot be more than 1024
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
#ifdef SPLIT_LV
pound_mis = 0;
if(pound_pos_1_f >= s_r_o_r1) //1
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f < pound_pos_1_r)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r1;
}
else if(pound_pos_1_r <= s_r_o_l1 + 1) //5
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_r > 0)
{
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r1;
}
else if((pound_pos_1_f <= s_r_o_l1 + 1) && (pound_pos_1_r >= s_r_o_r1)) //2
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i <= s_r_o_l1) && (bit_char_i_ref <= s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f <= s_r_o_l1)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = s_r_o_l1 >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = (s_r_o_l1 & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
}
else if((pound_pos_1_f > s_r_o_l1 + 1) && (pound_pos_1_f < s_r_o_r1)) //3
{
#ifdef POUND_MIS
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
}
else //pound_pos_1_r > s_r_o_l1) && (pound_pos_1_r < s_r_o_r1)//4
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < s_r_o_l1) && (bit_char_i_ref < s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_l1 > 0)
{
read_pos_end_num = (s_r_o_l1 - 1) >> 5;
read_pos_end_re = ((s_r_o_l1 - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
#ifdef POUND_MODIFY
lv_down_left = s_r_o_r1;
#else
lv_down_left = s_r_o_l1;
#endif
}
#ifdef QUAL_FILT_LV
#ifdef QUAL_FILT_LV_MIS
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance_mis(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length_a1 - lv_up_right);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], qual_filt_lv_1 + lv_down_left);
dm1 = dm_l1 + dm_r1 + pound_mis;
dm_cir_1 = dm_l1 + dm_r1;// + pound_mis
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance_misboth(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], L_mis[tid], qual_filt_lv_1_o + read_length_a1 - lv_up_right, &mis_n1);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance_misboth(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], L_mis[tid], qual_filt_lv_1 + lv_down_left, &mis_n2);
dm1 = mis_n1 + mis_n2 + pound_mis;
dm_cir_1 = dm_l1 + dm_r1;// + pound_mis
#endif
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#else
#ifdef LAST_CIRCLE_NOPOUND
pound_mis = 0;
#endif
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid]);
//lv_x_r = (dm_l1 == -1) ? lv_dmt1 : lv_dmt1 - dm_l1;
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid]);
dm1 = dm_l1 + dm_r1 + pound_mis;
dm_cir_1 = dm_l1 + dm_r1;// + pound_mis
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
#endif
}
}
else
{
dm1 = mis_c_n;
dm_cir_1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1))
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch1[tid] - 1) dmt1 = 0;
}
else
{
dm1 = MAX_EDIT_SCORE;
dm_cir_1 = MAX_EDIT_SCORE;
}
//add the ref sequence at the end of queue
memcpy(cache_end1[q_rear1], ref_seq_tmp1[tid], ref_copy_num_chars_1);
cache_dis1[q_rear1] = dm1;
cache_dml1[q_rear1] = ld1;
cache_dmr1[q_rear1] = rd1;
cache_dm_cir1[q_rear1] = dm_cir_1;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
cache_kl1[q_rear1] = dm_l1;
cache_kr1[q_rear1] = dm_r1;
}
#endif
q_rear1 = ((q_rear1 + 1) & 0X1f);
++q_n1;
//add edit distance
}
}
//for end2
if((end2_uc_f == 0) && ((dmt2 <= d_l2) && (dmt2 <= d_r2))) // && (nuc2_f == 0)
{
if(nuc2_f == 0)
{
pos_l = mat_pos2[tid][r_i] - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp2[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars_2);
for(rst_i = 0; rst_i < ref_copy_num_2 - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp2[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp2[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp2[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp2[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp2[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp2[tid][rst_i] &= low_mask_2;
}
else
{
memcpy(ref_seq_tmp2[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars_2);
//clear the lowest n bit
ref_seq_tmp2[tid][ref_copy_num_2 - 1] &= low_mask_2;
}
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp2[tid][ref_copy_num_2 - 2];
ref_seq_tmp2[tid][ref_copy_num_2 - 2] &= low_mask_2;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num_2 - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp2[tid][rst_i] ^ read_bit_2[tid][read_b_i];
#ifdef QUAL_FILT
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_2[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch2[tid]) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch2[tid]) break;
#endif
}
ref_seq_tmp2[tid][ref_copy_num_2 - 2] = ref_tmp_ori;
//lv
if(mis_c_n_filt > max_mismatch2[tid])
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
for(bit_char_i = s_r_o_l2, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l2, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(s_r_o_l2 + 1, read_char[tid], 33 + s_r_o_l2, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r2 - s_r_o_l2, &dm_l2, &tle, >le, &gscore, &max_off);
for(bit_char_i = s_r_o_r2, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r2, read_b_i = 0; bit_char_i < read_length_2 + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(read_length_2 - s_r_o_r2, read_char[tid], 32 + read_length_2 - s_r_o_r2, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r2 - s_r_o_l2, &dm_r2, &tle, >le, &gscore, &max_off);
dm2 = MAX_OP_SCORE_P2 - (dm_l2 + dm_r2); //read length cannot be more than 1024
ld2 = s_r_o_l2;
rd2 = s_r_o_r2;
#endif
}
else
{
#ifdef SPLIT_LV
pound_mis = 0;
if(pound_pos_2_f >= s_r_o_r2) //1
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_2_f, bit_char_i_ref = pound_pos_2_f + 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_2_f < pound_pos_2_r)
{
read_pos_start_num = pound_pos_2_f >> 5;
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_re = (pound_pos_2_f & 0X1f) << 1;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l2;
lv_down_right = pound_pos_2_f;
lv_down_left = s_r_o_r2;
}
else if(pound_pos_2_r <= s_r_o_l2 + 1) //5
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_2_r > 0)
{
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_2[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_2[tid][0] ^ ref_seq_tmp2[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = pound_pos_2_r;
lv_up_right = s_r_o_l2;
lv_down_right = read_length_2;
lv_down_left = s_r_o_r2;
}
else if((pound_pos_2_f <= s_r_o_l2 + 1) && (pound_pos_2_r >= s_r_o_r2)) //2
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_2_f, bit_char_i_ref = pound_pos_2_f + 32; (bit_char_i <= s_r_o_l2) && (bit_char_i_ref <= s_r_o_l2 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
for(bit_char_i = s_r_o_r2, bit_char_i_ref = s_r_o_r2 + 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_2_f <= s_r_o_l2)
{
read_pos_start_num = pound_pos_2_f >> 5;
read_pos_end_num = s_r_o_l2 >> 5;
read_pos_re = (pound_pos_2_f & 0X1f) << 1;
read_pos_end_re = (s_r_o_l2 & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
if(s_r_o_r2 < pound_pos_2_r)
{
read_pos_start_num = s_r_o_r2 >> 5;
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_re = (s_r_o_r2 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = pound_pos_2_f - 1;
lv_down_right = read_length_2;
lv_down_left = pound_pos_2_r;
}
else if((pound_pos_2_f > s_r_o_l2 + 1) && (pound_pos_2_f < s_r_o_r2)) //3
{
#ifdef POUND_MIS
for(bit_char_i = s_r_o_r2, bit_char_i_ref = s_r_o_r2 + 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_r2 < pound_pos_2_r)
{
read_pos_start_num = s_r_o_r2 >> 5;
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_re = (s_r_o_r2 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l2;
lv_down_right = read_length_2;
lv_down_left = pound_pos_2_r;
}
else //4
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < s_r_o_l2) && (bit_char_i_ref < s_r_o_l2 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_l2 > 0)
{
read_pos_end_num = (s_r_o_l2 - 1) >> 5;
read_pos_end_re = ((s_r_o_l2 - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_2[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_2[tid][0] ^ ref_seq_tmp2[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_2;
#ifdef POUND_MODIFY
lv_down_left = s_r_o_r2;
#else
lv_down_left = s_r_o_l2;
#endif
}
#ifdef QUAL_FILT_LV
#ifdef QUAL_FILT_LV_MIS
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l2 = computeEditDistance_mis(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt2, L[tid], qual_filt_lv_2_o + read_length_a2 - lv_up_right);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r2 = computeEditDistance_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt2, L[tid], qual_filt_lv_2 + lv_down_left);
dm2 = dm_l2 + dm_r2 + pound_mis;
dm_cir_2 = dm_l2 + dm_r2;// + pound_mis
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l2 = computeEditDistance_misboth(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt2, L[tid], L_mis[tid], qual_filt_lv_2_o + read_length_a2 - lv_up_right, &mis_n1);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r2 = computeEditDistance_misboth(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt2, L[tid], L_mis[tid], qual_filt_lv_2 + lv_down_left, &mis_n2);
dm2 = mis_n1 + mis_n2 + pound_mis;
dm_cir_2 = dm_l2 + dm_r2;// + pound_mis
#endif
ld2 = s_r_o_l2;
rd2 = s_r_o_r2;
#else
#ifdef LAST_CIRCLE_NOPOUND
pound_mis = 0;
#endif
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l2 = computeEditDistance(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt2, L[tid]);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r2 = computeEditDistance(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt2, L[tid]);
dm2 = dm_l2 + dm_r2 + pound_mis;
dm_cir_2 = dm_l2 + dm_r2;// + pound_mis
ld2 = s_r_o_l2;
rd2 = s_r_o_r2;
#endif
#endif
}
}
else
{
dm2 = mis_c_n;
dm_cir_2 = mis_c_n;
ld2 = 0;
rd2 = 0;
dm_l2 = 0;
dm_r2 = 0;
}
//these two values could be different
if((dm_l2 != -1) && (dm_r2 != -1))
{
if(dm2 < dmt2) dmt2 = dm2 + 1;
if(dm2 < lv_dmt2) lv_dmt2 = dm2 + 1;
if(dm2 < max_mismatch2[tid] - 1) dmt2 = 0;
}
else
{
dm2 = MAX_EDIT_SCORE;
dm_cir_2 = MAX_EDIT_SCORE;
}
nuc2_f = 1;
}
}
else
{
pos_l = mat_pos2[tid][r_i] - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp2[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars_2);
for(rst_i = 0; rst_i < ref_copy_num_2 - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp2[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp2[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp2[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp2[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp2[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp2[tid][rst_i] &= low_mask_2;
}
else
{
memcpy(ref_seq_tmp2[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars_2);
//clear the lowest n bit
ref_seq_tmp2[tid][ref_copy_num_2 - 1] &= low_mask_2;
}
//trim the beginning and end of the current ref seq based on current minimum edit distance dm_t
s_m_t = sub_mask2[tid][dmt2];
ref_seq_tmp2[tid][0] &= bit_tran[dmt2];
ref_seq_tmp2[tid][s_m_t] &= ex_d_mask2[tid][dmt2];
//traverse and check whether there is an existing seq that is as same as current new ref seq
c_m_f = 0;
for(q_rear_i = q_rear2 - 1; q_rear_i >= 0; q_rear_i--)
{
ref_tmp_ori = cache_end2[q_rear_i][0];
cache_end2[q_rear_i][0] &= bit_tran[dmt2];
ref_tmp_ori2 = cache_end2[q_rear_i][s_m_t];
cache_end2[q_rear_i][s_m_t] &= ex_d_mask2[tid][dmt2];
cmp_re = memcmp(cache_end2[q_rear_i], ref_seq_tmp2[tid], (s_m_t + 1) << 3);
cache_end2[q_rear_i][0] = ref_tmp_ori;
cache_end2[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm2 = cache_dis2[q_rear_i];
ld2 = cache_dml2[q_rear_i];
rd2 = cache_dmr2[q_rear_i];
dm_cir_2 = cache_dm_cir2[q_rear_i];
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
dm_l2 = cache_kl2[q_rear_i];
dm_r2 = cache_kr2[q_rear_i];
}
#endif
c_m_f = 1;
break;
}
}
if((q_n2 > MAX_Q_NUM) && (q_rear_i < 0))
{
for(q_rear_i = MAX_Q_NUM - 1; q_rear_i >= q_rear2; q_rear_i--)
{
ref_tmp_ori = cache_end2[q_rear_i][0];
cache_end2[q_rear_i][0] &= bit_tran[dmt2];
ref_tmp_ori2 = cache_end2[q_rear_i][s_m_t];
cache_end2[q_rear_i][s_m_t] &= ex_d_mask2[tid][dmt2];
cmp_re = memcmp(cache_end2[q_rear_i], ref_seq_tmp2[tid], (s_m_t + 1) << 3);
cache_end2[q_rear_i][0] = ref_tmp_ori;
cache_end2[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm2 = cache_dis2[q_rear_i];
ld2 = cache_dml2[q_rear_i];
rd2 = cache_dmr2[q_rear_i];
dm_cir_2 = cache_dm_cir2[q_rear_i];
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
dm_l2 = cache_kl2[q_rear_i];
dm_r2 = cache_kr2[q_rear_i];
}
#endif
c_m_f = 1;
break;
}
}
}
//do not find the seq in cache, exact match or lv and add into cache
if(c_m_f == 0)
{
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp2[tid][ref_copy_num_2 - 2];
ref_seq_tmp2[tid][ref_copy_num_2 - 2] &= low_mask_2;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num_2 - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp2[tid][rst_i] ^ read_bit_2[tid][read_b_i];
#ifdef QUAL_FILT
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_2[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch2[tid]) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch2[tid]) break;
#endif
}
ref_seq_tmp2[tid][ref_copy_num_2 - 2] = ref_tmp_ori;
//lv
if(mis_c_n_filt > max_mismatch2[tid])
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
for(bit_char_i = s_r_o_l2, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l2, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(s_r_o_l2 + 1, read_char[tid], 33 + s_r_o_l2, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r2 - s_r_o_l2, &dm_l2, &tle, >le, &gscore, &max_off);
for(bit_char_i = s_r_o_r2, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r2, read_b_i = 0; bit_char_i < read_length_2 + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(read_length_2 - s_r_o_r2, read_char[tid], 32 + read_length_2 - s_r_o_r2, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r2 - s_r_o_l2, &dm_r2, &tle, >le, &gscore, &max_off);
dm2 = MAX_OP_SCORE_P2 - (dm_l2 + dm_r2); //read length cannot be more than 1024
ld2 = s_r_o_l2;
rd2 = s_r_o_r2;
#endif
}
else
{
#ifdef SPLIT_LV
pound_mis = 0;
if(pound_pos_2_f >= s_r_o_r2) //1
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_2_f, bit_char_i_ref = pound_pos_2_f + 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_2_f < pound_pos_2_r)
{
read_pos_start_num = pound_pos_2_f >> 5;
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_re = (pound_pos_2_f & 0X1f) << 1;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l2;
lv_down_right = pound_pos_2_f;
lv_down_left = s_r_o_r2;
}
else if(pound_pos_2_r <= s_r_o_l2 + 1) //5
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_2_r > 0)
{
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_2[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_2[tid][0] ^ ref_seq_tmp2[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = pound_pos_2_r;
lv_up_right = s_r_o_l2;
lv_down_right = read_length_2;
lv_down_left = s_r_o_r2;
}
else if((pound_pos_2_f <= s_r_o_l2 + 1) && (pound_pos_2_r >= s_r_o_r2)) //2
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_2_f, bit_char_i_ref = pound_pos_2_f + 32; (bit_char_i <= s_r_o_l2) && (bit_char_i_ref <= s_r_o_l2 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
for(bit_char_i = s_r_o_r2, bit_char_i_ref = s_r_o_r2 + 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_2_f <= s_r_o_l2)
{
read_pos_start_num = pound_pos_2_f >> 5;
read_pos_end_num = s_r_o_l2 >> 5;
read_pos_re = (pound_pos_2_f & 0X1f) << 1;
read_pos_end_re = (s_r_o_l2 & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
if(s_r_o_r2 < pound_pos_2_r)
{
read_pos_start_num = s_r_o_r2 >> 5;
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_re = (s_r_o_r2 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = pound_pos_2_f - 1;
lv_down_right = read_length_2;
lv_down_left = pound_pos_2_r;
}
else if((pound_pos_2_f > s_r_o_l2 + 1) && (pound_pos_2_f < s_r_o_r2)) //3
{
#ifdef POUND_MIS
for(bit_char_i = s_r_o_r2, bit_char_i_ref = s_r_o_r2 + 32; (bit_char_i < pound_pos_2_r) && (bit_char_i_ref < pound_pos_2_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_r2 < pound_pos_2_r)
{
read_pos_start_num = s_r_o_r2 >> 5;
read_pos_end_num = (pound_pos_2_r - 1) >> 5;
read_pos_re = (s_r_o_r2 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_2_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_2[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_2[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp2[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l2;
lv_down_right = read_length_2;
lv_down_left = pound_pos_2_r;
}
else //4
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < s_r_o_l2) && (bit_char_i_ref < s_r_o_l2 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp2[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_l2 > 0)
{
read_pos_end_num = (s_r_o_l2 - 1) >> 5;
read_pos_end_re = ((s_r_o_l2 - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_2[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_2[tid][0] ^ ref_seq_tmp2[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_2[tid][rst_i] ^ ref_seq_tmp2[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_2[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp2[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_2;
#ifdef POUND_MODIFY
lv_down_left = s_r_o_r2;
#else
lv_down_left = s_r_o_l2;
#endif
}
#ifdef QUAL_FILT_LV
#ifdef QUAL_FILT_LV_MIS
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#ifdef S_DEBUG
printf("extension lv2 %u: %u %d %d\n", mat_rc[tid][r_i], lv_dmt2, lv_up_right, lv_up_left);
#endif
dm_l2 = computeEditDistance_mis(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt2, L[tid], qual_filt_lv_2_o + read_length_a2 - lv_up_right);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r2 = computeEditDistance_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt2, L[tid], qual_filt_lv_2 + lv_down_left);
dm2 = dm_l2 + dm_r2 + pound_mis;
dm_cir_2 = dm_l2 + dm_r2;// + pound_mis
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l2 = computeEditDistance_misboth(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt2, L[tid], L_mis[tid], qual_filt_lv_2_o + read_length_a2 - lv_up_right, &mis_n1);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r2 = computeEditDistance_misboth(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt2, L[tid], L_mis[tid], qual_filt_lv_2 + lv_down_left, &mis_n2);
dm2 = mis_n1 + mis_n2 + pound_mis;
dm_cir_2 = dm_l2 + dm_r2;// + pound_mis
#endif
ld2 = s_r_o_l2;
rd2 = s_r_o_r2;
#else
#ifdef LAST_CIRCLE_NOPOUND
pound_mis = 0;
#endif
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l2 = computeEditDistance(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt2, L[tid]);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r2 = computeEditDistance(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt2, L[tid]);
dm2 = dm_l2 + dm_r2 + pound_mis;
dm_cir_2 = dm_l2 + dm_r2;// + pound_mis
ld2 = s_r_o_l2;
rd2 = s_r_o_r2;
#endif
#endif
}
}
else
{
dm2 = mis_c_n;
dm_cir_2 = mis_c_n;
ld2 = 0;
rd2 = 0;
dm_l2 = 0;
dm_r2 = 0;
}
//these two values could be different
if((dm_l2 != -1) && (dm_r2 != -1))
{
if(dm2 < dmt2) dmt2 = dm2 + 1;
if(dm2 < lv_dmt2) lv_dmt2 = dm2 + 1;
if(dm2 < max_mismatch2[tid] - 1) dmt2 = 0;
}
else
{
dm2 = MAX_EDIT_SCORE;
dm_cir_2 = MAX_EDIT_SCORE;
}
//add the ref sequence at the end of queue
memcpy(cache_end2[q_rear2], ref_seq_tmp2[tid], ref_copy_num_chars_2);
cache_dis2[q_rear2] = dm2;
//cache_lvf1[q_rear1] = lv_f1;
cache_dml2[q_rear2] = ld2;
cache_dmr2[q_rear2] = rd2;
cache_dm_cir2[q_rear2] = dm_cir_2;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
cache_kl2[q_rear2] = dm_l2;
cache_kr2[q_rear2] = dm_r2;
}
#endif
q_rear2 = ((q_rear2 + 1) & 0X1f);
++q_n2;
//add edit distance
}
}
#endif
dm_cir = dm_cir_1 + dm_cir_2;
if(dm_cir < dm_cir_min) dm_cir_min = dm_cir;
dm12 = dm1 + dm2;
if(dm12 < dm_op[tid])
{
#ifdef DM_COPY_PAIR
for(dm_i = 0; dm_i < v_cnt; dm_i++)
{
ops_vector_pos1[tid][dm_i] = op_vector_pos1[tid][dm_i];
ops_dm_l1[tid][dm_i] = op_dm_l1[tid][dm_i];
ops_dm_r1[tid][dm_i] = op_dm_r1[tid][dm_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars1);
#else
if(!((op_dm_l1[tid][dm_i] == 0) && (op_dm_r1[tid][dm_i] == 0)))
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars1);
#endif
ops_dm_ex1[tid][dm_i] = op_dm_ex1[tid][dm_i];
ops_vector_pos2[tid][dm_i] = op_vector_pos2[tid][dm_i];
ops_dm_l2[tid][dm_i] = op_dm_l2[tid][dm_i];
ops_dm_r2[tid][dm_i] = op_dm_r2[tid][dm_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq2[tid][dm_i], op_vector_seq2[tid][dm_i], ref_copy_num_chars2);
#else
if(!((op_dm_l2[tid][dm_i] == 0) && (op_dm_r2[tid][dm_i] == 0)))
memcpy(ops_vector_seq2[tid][dm_i], op_vector_seq2[tid][dm_i], ref_copy_num_chars2);
#endif
ops_dm_ex2[tid][dm_i] = op_dm_ex2[tid][dm_i];
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
ops_dm_kl1[tid][dm_i] = op_dm_kl1[tid][dm_i];
ops_dm_kr1[tid][dm_i] = op_dm_kr1[tid][dm_i];
ops_dm_kl2[tid][dm_i] = op_dm_kl2[tid][dm_i];
ops_dm_kr2[tid][dm_i] = op_dm_kr2[tid][dm_i];
}
#endif
ops_rc[tid][dm_i] = op_rc[tid][dm_i];
}
vs_cnt = v_cnt;
dm_ops[tid] = dm_op[tid];
#endif
v_cnt = 0;
if(mat_rc[tid][r_i] == 0)
{
op_vector_pos1[tid][v_cnt] = mat_pos1[tid][r_i];
op_vector_pos2[tid][v_cnt] = mat_pos2[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
op_dm_l2[tid][v_cnt] = ld2;
op_dm_r2[tid][v_cnt] = rd2;
op_dm_ex1[tid][v_cnt] = dm1;
op_dm_ex2[tid][v_cnt] = dm2;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
op_dm_kl1[tid][v_cnt] = dm_l1;
op_dm_kr1[tid][v_cnt] = dm_r1;
op_dm_kl2[tid][v_cnt] = dm_l2;
op_dm_kr2[tid][v_cnt] = dm_r2;
}
#endif
}
else
{
op_vector_pos1[tid][v_cnt] = mat_pos2[tid][r_i];
op_vector_pos2[tid][v_cnt] = mat_pos1[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld2;
op_dm_r1[tid][v_cnt] = rd2;
op_dm_l2[tid][v_cnt] = ld1;
op_dm_r2[tid][v_cnt] = rd1;
op_dm_ex1[tid][v_cnt] = dm2;
op_dm_ex2[tid][v_cnt] = dm1;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
op_dm_kl1[tid][v_cnt] = dm_l2;
op_dm_kr1[tid][v_cnt] = dm_r2;
op_dm_kl2[tid][v_cnt] = dm_l1;
op_dm_kr2[tid][v_cnt] = dm_r1;
}
#endif
}
#ifdef ALTER_DEBUG
seed_length_arr[tid][v_cnt].seed_length = seed_length1 + seed_length2;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
op_rc[tid][v_cnt] = mat_rc[tid][r_i];
++v_cnt;
dm_op[tid] = dm12;
}
else if(dm12 == dm_op[tid])
{
if(v_cnt < cus_max_output_ali)
{
if(mat_rc[tid][r_i] == 0)
{
op_vector_pos1[tid][v_cnt] = mat_pos1[tid][r_i];
op_vector_pos2[tid][v_cnt] = mat_pos2[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
op_dm_l2[tid][v_cnt] = ld2;
op_dm_r2[tid][v_cnt] = rd2;
op_dm_ex1[tid][v_cnt] = dm1;
op_dm_ex2[tid][v_cnt] = dm2;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
op_dm_kl1[tid][v_cnt] = dm_l1;
op_dm_kr1[tid][v_cnt] = dm_r1;
op_dm_kl2[tid][v_cnt] = dm_l2;
op_dm_kr2[tid][v_cnt] = dm_r2;
}
#endif
}
else
{
op_vector_pos1[tid][v_cnt] = mat_pos2[tid][r_i];
op_vector_pos2[tid][v_cnt] = mat_pos1[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld2;
op_dm_r1[tid][v_cnt] = rd2;
op_dm_l2[tid][v_cnt] = ld1;
op_dm_r2[tid][v_cnt] = rd1;
op_dm_ex1[tid][v_cnt] = dm2;
op_dm_ex2[tid][v_cnt] = dm1;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
op_dm_kl1[tid][v_cnt] = dm_l2;
op_dm_kr1[tid][v_cnt] = dm_r2;
op_dm_kl2[tid][v_cnt] = dm_l1;
op_dm_kr2[tid][v_cnt] = dm_r1;
}
#endif
}
#ifdef ALTER_DEBUG
seed_length_arr[tid][v_cnt].seed_length = seed_length1 + seed_length2;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
op_rc[tid][v_cnt] = mat_rc[tid][r_i];
++v_cnt;
}
}
else if(dm12 < dm_ops[tid])
{
vs_cnt = 0;
if(mat_rc[tid][r_i] == 0)
{
ops_vector_pos1[tid][vs_cnt] = mat_pos1[tid][r_i];
ops_vector_pos2[tid][vs_cnt] = mat_pos2[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
ops_dm_l2[tid][vs_cnt] = ld2;
ops_dm_r2[tid][vs_cnt] = rd2;
ops_dm_ex1[tid][vs_cnt] = dm1;
ops_dm_ex2[tid][vs_cnt] = dm2;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
ops_dm_kl1[tid][vs_cnt] = dm_l1;
ops_dm_kr1[tid][vs_cnt] = dm_r1;
ops_dm_kl2[tid][vs_cnt] = dm_l2;
ops_dm_kr2[tid][vs_cnt] = dm_r2;
}
#endif
}
else
{
ops_vector_pos1[tid][vs_cnt] = mat_pos2[tid][r_i];
ops_vector_pos2[tid][vs_cnt] = mat_pos1[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld2;
ops_dm_r1[tid][vs_cnt] = rd2;
ops_dm_l2[tid][vs_cnt] = ld1;
ops_dm_r2[tid][vs_cnt] = rd1;
ops_dm_ex1[tid][vs_cnt] = dm2;
ops_dm_ex2[tid][vs_cnt] = dm1;
//for S
#ifdef QUALS_CHECK
ops_err[tid][vs_cnt] = error_f;
#endif
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
ops_dm_kl1[tid][vs_cnt] = dm_l2;
ops_dm_kr1[tid][vs_cnt] = dm_r2;
ops_dm_kl2[tid][vs_cnt] = dm_l1;
ops_dm_kr2[tid][vs_cnt] = dm_r1;
}
#endif
}
ops_rc[tid][vs_cnt] = mat_rc[tid][r_i];
++vs_cnt;
dm_ops[tid] = dm12;
}
else if(dm12 == dm_ops[tid])
{
if(vs_cnt < cus_max_output_ali)
{
if(mat_rc[tid][r_i] == 0)
{
ops_vector_pos1[tid][vs_cnt] = mat_pos1[tid][r_i];
ops_vector_pos2[tid][vs_cnt] = mat_pos2[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
ops_dm_l2[tid][vs_cnt] = ld2;
ops_dm_r2[tid][vs_cnt] = rd2;
ops_dm_ex1[tid][vs_cnt] = dm1;
ops_dm_ex2[tid][vs_cnt] = dm2;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
ops_dm_kl1[tid][vs_cnt] = dm_l1;
ops_dm_kr1[tid][vs_cnt] = dm_r1;
ops_dm_kl2[tid][vs_cnt] = dm_l2;
ops_dm_kr2[tid][vs_cnt] = dm_r2;
}
#endif
}
else
{
ops_vector_pos1[tid][vs_cnt] = mat_pos2[tid][r_i];
ops_vector_pos2[tid][vs_cnt] = mat_pos1[tid][r_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld2;
ops_dm_r1[tid][vs_cnt] = rd2;
ops_dm_l2[tid][vs_cnt] = ld1;
ops_dm_r2[tid][vs_cnt] = rd1;
ops_dm_ex1[tid][vs_cnt] = dm2;
ops_dm_ex2[tid][vs_cnt] = dm1;
#ifdef KSW_ALN_PAIR
if(local_ksw)
{
ops_dm_kl1[tid][vs_cnt] = dm_l2;
ops_dm_kr1[tid][vs_cnt] = dm_r2;
ops_dm_kl2[tid][vs_cnt] = dm_l1;
ops_dm_kr2[tid][vs_cnt] = dm_r1;
}
#endif
}
ops_rc[tid][vs_cnt] = mat_rc[tid][r_i];
++vs_cnt;
}
}
}
if(local_ksw)
{
if((dm_cir_min > max_pair_score) && (cir_n != cir_fix_n))
{
seed_l[tid] -= seed_step;
cir_n = cir_fix_n;
continue;
}
}
else
{
if(dm_cir_min > max_pair_score)
{
seed_l[tid] -= seed_step;
cir_n++;
#ifdef CIR_JUMP
if(last_circle_rate)
{
lv_k1 = (read_length1 * last_circle_rate);
lv_k2 = (read_length2 * last_circle_rate);
max_pair_score = (read_length1 + read_length2) * last_circle_rate;
}
#endif
continue;
}
}
#ifdef ALI_OUT
seqio[seqi].v_cnt = v_cnt;
if(v_cnt > 0)
{
#ifdef ALTER_DEBUG
if(v_cnt > 1) qsort(seed_length_arr[tid], v_cnt, sizeof(seed_length_array), compare_seed_length);
#endif
de_m_p_o[tid] = 0;
#ifdef PR_SINGLE
pr_o_f[tid] = 0;
#endif
cnt.v_cnt = v_cnt;
cnt.vs_cnt = vs_cnt;
pair_sam_output(tid, read_length1, read_length2, f_cigarn, &cnt, seqi, lv_k1, lv_k2, pound_pos1_f_forward, pound_pos1_f_reverse, pound_pos1_r_forward, pound_pos1_r_reverse, pound_pos2_f_forward, pound_pos2_f_reverse, pound_pos2_r_forward, pound_pos2_r_reverse, cir_n);
}
#endif
break;
}
cir_n++;
}
#ifdef PAIR_RANDOM
#ifdef PR_COV_FILTER
if((((pos_ren[0][0][tid] > 0) && (pos_ren[0][1][tid] > 0)) || ((pos_ren[1][0][tid] > 0) && (pos_ren[1][1][tid] > 0))) && (de_m_p_o[tid] == 1) && (cov_filt_f[tid] == 0))
#else
if((((pos_ren[0][0][tid] > 0) && (pos_ren[0][1][tid] > 0)) || ((pos_ren[1][0][tid] > 0) && (pos_ren[1][1][tid] > 0))) && (de_m_p_o[tid] == 1))
#endif
{
#ifdef PR_SINGLE
seed_re_r[tid] = 1;
#endif
#ifdef ALTER_DEBUG
rep_go[tid] = 0;
#endif
seed_repetitive(tid, read_length1, read_length2, f_cigarn, ref_copy_num1, ref_copy_num2, ref_copy_num_chars1, ref_copy_num_chars2, &cnt, seqi, lv_k1, lv_k2, pound_pos1_f_forward, pound_pos1_f_reverse, pound_pos1_r_forward, pound_pos1_r_reverse, pound_pos2_f_forward, pound_pos2_f_reverse, pound_pos2_r_forward, pound_pos2_r_reverse);
}
#endif
//deal with unmatched reads
#ifdef UNMATCH_SINGLE_END
if(de_m_p_o[tid] == 1)
{
#ifdef SINGLE_END_NOEXECUTE
dm_op[tid] = MAX_OP_SCORE;
dm_ops[tid] = MAX_OP_SCORE;
v_cnt = 0;
vs_cnt = 0;
lv_k1 = (read_length1 * lv_rate_anchor) + 1;//lv_rate
lv_k2 = (read_length2 * lv_rate_anchor) + 1;//lv_rate
#ifdef SEED_FILTER_LENGTH
max_sets_n[0][0] = (max_read_length[0][0] > max_read_length[1][1]) ? max_read_length[0][0]:max_read_length[1][1];
max_sets_n[0][1] = (max_read_length[0][1] > max_read_length[1][0]) ? max_read_length[0][1]:max_read_length[1][0];
max_sets_n[1][1] = max_sets_n[0][0];
max_sets_n[1][0] = max_sets_n[0][1];
#endif
for(rc_i = 0; rc_i < 2; rc_i++)
{
for(un_ii = 0; un_ii < 2; un_ii++)
{
if(unmatch[rc_i][un_ii] == 1) continue;
seed_pr1 = seed_pr[rc_i][un_ii];
#ifdef SEED_FILTER_LENGTH
for(off_i = 0; off_i < spa_i[rc_i][un_ii]; off_i++)
if(seed_pr1[off_i].length < max_sets_n[rc_i][un_ii] - length_reduce)
{
++off_i;
break;
}
spa_i[rc_i][un_ii] = off_i;
#endif
#ifdef SEED_FILTER_POS
qsort(seed_pr1, spa_i[rc_i][un_ii], sizeof(seed_pa), compare_seed_filter_posn);
seed_posn_filter = 0;
#endif
#ifdef SEED_FILTER
single_lv_re = 0;
#endif
if(rc_i == 0)
{
if(un_ii == 0)
{
read_bit_1[tid] = read_bit1[tid][0];
#ifdef QUAL_FILT_SINGLE
qual_filt_1 = qual_filt1[tid][0];
#endif
#ifdef QUAL_FILT_LV_SINGLE
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
ref_copy_num_chars = ref_copy_num_chars1;
ref_copy_num = ref_copy_num1;
low_mask = low_mask1[tid];
sub_mask = sub_mask1[tid];
ex_d_mask = ex_d_mask1[tid];
max_mismatch = max_mismatch1_single[tid];
lv_k = lv_k1;
read_length = read_length1;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
}
else
{
read_bit_1[tid] = read_bit2[tid][1];
#ifdef QUAL_FILT_SINGLE
qual_filt_1 = qual_filt2[tid][1];
#endif
#ifdef QUAL_FILT_LV_SINGLE
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
ref_copy_num_chars = ref_copy_num_chars2;
ref_copy_num = ref_copy_num2;
low_mask = low_mask2[tid];
sub_mask = sub_mask2[tid];
ex_d_mask = ex_d_mask2[tid];
max_mismatch = max_mismatch2_single[tid];
lv_k = lv_k2;
read_length = read_length2;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
}
}
else
{
if(un_ii == 0)
{
read_bit_1[tid] = read_bit2[tid][0];
#ifdef QUAL_FILT_SINGLE
qual_filt_1 = qual_filt2[tid][0];
#endif
#ifdef QUAL_FILT_LV_SINGLE
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
ref_copy_num_chars = ref_copy_num_chars2;
ref_copy_num = ref_copy_num2;
low_mask = low_mask2[tid];
sub_mask = sub_mask2[tid];
ex_d_mask = ex_d_mask2[tid];
max_mismatch = max_mismatch2_single[tid];
lv_k = lv_k2;
read_length = read_length2;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
}
else
{
read_bit_1[tid] = read_bit1[tid][1];
#ifdef QUAL_FILT_SINGLE
qual_filt_1 = qual_filt1[tid][1];
#endif
#ifdef QUAL_FILT_LV_SINGLE
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
ref_copy_num_chars = ref_copy_num_chars1;
ref_copy_num = ref_copy_num1;
low_mask = low_mask1[tid];
sub_mask = sub_mask1[tid];
ex_d_mask = ex_d_mask1[tid];
max_mismatch = max_mismatch1_single[tid];
lv_k = lv_k1;
read_length = read_length1;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
}
}
for(seed1_i = 0; seed1_i < spa_i[rc_i][un_ii]; seed1_i++)
{
#ifdef SEED_FILTER
if(seed_pr1[seed1_i].length > (read_length >> 1)) single_lv_re = 1;
else
{
if(single_lv_re == 1) continue;
}
#endif
if(seed_pr1[seed1_i].ui == 1)
{
end1_uc_f = 0;
nuc1_f = 0;
d_l1 = seed_pr1[seed1_i].ref_pos_off;
d_r1 = seed_pr1[seed1_i].ref_pos_off_r;
}
else
{
end1_uc_f = 1;
}
q_rear1 = 0;
q_n1 = 0;
dmt1 = ali_exl;
lv_dmt1 = lv_k;
s_r_o_l1 = seed_pr1[seed1_i].s_r_o_l;
s_r_o_r1 = seed_pr1[seed1_i].s_r_o_r;
#ifdef ALTER_DEBUG_ANCHOR
seed_length1 = seed_pr1[seed1_i].length;
#endif
for(psp_i = 0; psp_i < seed_pr1[seed1_i].pos_n; psp_i++)
{
#ifdef SEED_FILTER_POS
if(seed_posn_filter > seed_filter_pos_num) break;
seed_posn_filter++;
#endif
posi = seed_set_pos[rc_i][un_ii][tid][seed_pr1[seed1_i].pos_start + psp_i];
#ifdef ANCHOR_LV_S
s_offset_l = 0;
s_offset_r = 0;
#endif
//for end1
if((end1_uc_f == 0) && ((dmt1 <= d_l1) && (dmt1 <= d_r1))) // && (nuc1_f == 0)
{
if(nuc1_f == 0)
{
pos_l = posi - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars);
for(rst_i = 0; rst_i < ref_copy_num - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask;
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num - 1] &= low_mask;
}
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT_SINGLE
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num - 2];
ref_seq_tmp1[tid][ref_copy_num - 2] &= low_mask;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT_SINGLE
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch) break;
#endif
}
ref_seq_tmp1[tid][ref_copy_num - 2] = ref_tmp_ori;
//dm = mis_c_n;
//lv
if(mis_c_n_filt > max_mismatch)
{
#ifdef SPLIT_LV
pound_mis = 0;
if(pound_pos_1_f >= s_r_o_r1) //1
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f < pound_pos_1_r)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r1;
}
else if(pound_pos_1_r <= s_r_o_l1 + 1) //5
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_r > 0)
{
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = pound_pos_1_r;
lv_up_right = s_r_o_l1;
lv_down_right = read_length;
lv_down_left = s_r_o_r1;
}
else if((pound_pos_1_f <= s_r_o_l1 + 1) && (pound_pos_1_r >= s_r_o_r1)) //2
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i <= s_r_o_l1) && (bit_char_i_ref <= s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f <= s_r_o_l1)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = s_r_o_l1 >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = (s_r_o_l1 & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length;
lv_down_left = pound_pos_1_r;
}
else if((pound_pos_1_f > s_r_o_l1 + 1) && (pound_pos_1_f < s_r_o_r1)) //3
{
#ifdef POUND_MIS
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = read_length;
lv_down_left = pound_pos_1_r;
}
else //4
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < s_r_o_l1) && (bit_char_i_ref < s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_l1 > 0)
{
read_pos_end_num = (s_r_o_l1 - 1) >> 5;
read_pos_end_re = ((s_r_o_l1 - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length;
#ifdef POUND_MODIFY
lv_down_left = s_r_o_r1;
#else
lv_down_left = s_r_o_l1;
#endif
}
#ifdef QUAL_FILT_LV_SINGLE
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#ifdef ANCHOR_LV_S
dm_l1 = computeEditDistance_mis_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length - 1 - lv_up_right, &s_offset_l);
#else
dm_l1 = computeEditDistance_mis(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length - 1 - lv_up_right);
#endif
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#ifdef ANCHOR_LV_S
dm_r1 = computeEditDistance_mis_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], qual_filt_lv_1 + lv_down_left, &s_offset_r);
#else
dm_r1 = computeEditDistance_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], qual_filt_lv_1 + lv_down_left);
#endif
dm1 = dm_l1 + dm_r1 + pound_mis;
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid]);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid]);
dm1 = dm_l1 + dm_r1 + pound_mis;
#endif
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
dm1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1))
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch - 1) dmt1 = 0;
}
else
{
#ifdef ANCHOR_LV_S
if((s_offset_l + s_offset_r) < ((float )read_length * ANCHOR_LV_S_FLOAT))
dm1 = lv_dmt1 + pound_mis;
else dm1 = MAX_EDIT_SCORE;
#else
dm1 = MAX_EDIT_SCORE;
#endif
}
nuc1_f = 1;
}
}
else
{
pos_l = posi - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars);
for(rst_i = 0; rst_i < ref_copy_num - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask;
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num - 1] &= low_mask;
}
//trim the beginning and end of the current ref seq based on current minimum edit distance dm_t
s_m_t = sub_mask[dmt1];
ref_seq_tmp1[tid][0] &= bit_tran[dmt1];
ref_seq_tmp1[tid][s_m_t] &= ex_d_mask[dmt1];
//traverse and check whether there is an existing seq that is as same as current new ref seq
c_m_f = 0;
for(q_rear_i = q_rear1 - 1; q_rear_i >= 0; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask[dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
c_m_f = 1;
break;
}
}
if((q_n1 > MAX_Q_NUM) && (q_rear_i < 0))
{
for(q_rear_i = MAX_Q_NUM - 1; q_rear_i >= q_rear1; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask[dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
c_m_f = 1;
break;
}
}
}
//do not find the seq in cache, exact match or lv and add into cache
if(c_m_f == 0)
{
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT_SINGLE
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num - 2];
ref_seq_tmp1[tid][ref_copy_num - 2] &= low_mask;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT_SINGLE
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch) break;
#endif
}
ref_seq_tmp1[tid][ref_copy_num - 2] = ref_tmp_ori;
//lv
if(mis_c_n_filt > max_mismatch)
{
#ifdef SPLIT_LV
pound_mis = 0;
if(pound_pos_1_f >= s_r_o_r1) //1
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f < pound_pos_1_r)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r1;
}
else if(pound_pos_1_r <= s_r_o_l1 + 1) //5
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_r > 0)
{
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = pound_pos_1_r;
lv_up_right = s_r_o_l1;
lv_down_right = read_length;
lv_down_left = s_r_o_r1;
}
else if((pound_pos_1_f <= s_r_o_l1 + 1) && (pound_pos_1_r >= s_r_o_r1)) //2
{
#ifdef POUND_MIS
for(bit_char_i = pound_pos_1_f, bit_char_i_ref = pound_pos_1_f + 32; (bit_char_i <= s_r_o_l1) && (bit_char_i_ref <= s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(pound_pos_1_f <= s_r_o_l1)
{
read_pos_start_num = pound_pos_1_f >> 5;
read_pos_end_num = s_r_o_l1 >> 5;
read_pos_re = (pound_pos_1_f & 0X1f) << 1;
read_pos_end_re = (s_r_o_l1 & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length;
lv_down_left = pound_pos_1_r;
}
else if((pound_pos_1_f > s_r_o_l1 + 1) && (pound_pos_1_f < s_r_o_r1)) //3
{
#ifdef POUND_MIS
for(bit_char_i = s_r_o_r1, bit_char_i_ref = s_r_o_r1 + 32; (bit_char_i < pound_pos_1_r) && (bit_char_i_ref < pound_pos_1_r + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_r1 < pound_pos_1_r)
{
read_pos_start_num = s_r_o_r1 >> 5;
read_pos_end_num = (pound_pos_1_r - 1) >> 5;
read_pos_re = (s_r_o_r1 & 0X1f) << 1;
read_pos_end_re = ((pound_pos_1_r - 1) & 0X1f) << 1;
if(read_pos_start_num == read_pos_end_num)
{
xor_tmp = ((read_bit_1[tid][read_pos_start_num] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re)) ^ ((ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re) >> (62 - read_pos_end_re + read_pos_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = (read_bit_1[tid][read_pos_start_num] << read_pos_re) ^ (ref_seq_tmp1[tid][read_pos_start_num + 1] << read_pos_re);
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = read_pos_start_num + 1, rst_i_1 = read_pos_start_num + 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = s_r_o_l1;
lv_down_right = read_length;
lv_down_left = pound_pos_1_r;
}
else //4
{
#ifdef POUND_MIS
for(bit_char_i = 0, bit_char_i_ref = 32; (bit_char_i < s_r_o_l1) && (bit_char_i_ref < s_r_o_l1 + 32); bit_char_i++, bit_char_i_ref++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ref_seq_tmp1[tid][bit_char_i_ref >> 5] >> ((31 - (bit_char_i_ref & 0X1f)) << 1)) & 0X3))
pound_mis++;
#else
if(s_r_o_l1 > 0)
{
read_pos_end_num = (s_r_o_l1 - 1) >> 5;
read_pos_end_re = ((s_r_o_l1 - 1) & 0X1f) << 1;
if(read_pos_end_num == 0)
{
xor_tmp = (read_bit_1[tid][0] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
else
{
xor_tmp = read_bit_1[tid][0] ^ ref_seq_tmp1[tid][1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
for(rst_i = 1, rst_i_1 = 2; rst_i < read_pos_end_num; rst_i++, rst_i_1++)
{
xor_tmp = read_bit_1[tid][rst_i] ^ ref_seq_tmp1[tid][rst_i_1];
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
xor_tmp = (read_bit_1[tid][read_pos_end_num] >> (62 - read_pos_end_re)) ^ (ref_seq_tmp1[tid][read_pos_end_num + 1] >> (62 - read_pos_end_re));
pound_mis += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
}
}
#endif
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length;
#ifdef POUND_MODIFY
lv_down_left = s_r_o_r1;
#else
lv_down_left = s_r_o_l1;
#endif
}
#ifdef QUAL_FILT_LV_SINGLE
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#ifdef ANCHOR_LV_S
dm_l1 = computeEditDistance_mis_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length - 1 - lv_up_right, &s_offset_l);
#else
dm_l1 = computeEditDistance_mis(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length - 1 - lv_up_right);
#endif
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#ifdef ANCHOR_LV_S
dm_r1 = computeEditDistance_mis_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], qual_filt_lv_1 + lv_down_left, &s_offset_r);
#else
dm_r1 = computeEditDistance_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid], qual_filt_lv_1 + lv_down_left);
#endif
dm1 = dm_l1 + dm_r1 + pound_mis;
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_dmt1, L[tid]);
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_dmt1, L[tid]);
dm1 = dm_l1 + dm_r1 + pound_mis;
#endif
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
dm1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1))
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch - 1) dmt1 = 0;
}
else
{
#ifdef ANCHOR_LV_S
if((s_offset_l + s_offset_r) < ((float )read_length * ANCHOR_LV_S_FLOAT))
dm1 = lv_dmt1 + pound_mis;
else dm1 = MAX_EDIT_SCORE;
#else
dm1 = MAX_EDIT_SCORE;
#endif
}
//add the ref sequence at the end of queue
memcpy(cache_end1[q_rear1], ref_seq_tmp1[tid], ref_copy_num_chars);
cache_dis1[q_rear1] = dm1;
cache_dml1[q_rear1] = ld1;
cache_dmr1[q_rear1] = rd1;
q_rear1 = ((q_rear1 + 1) & 0X1f);
++q_n1;
//add edit distance
}
}
/*
x = posi;
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
posi = x - chr_end_n[chr_re - 1] + 1;
fprintf(stderr, "to add: %u %u %d %d %d rc: %u\n", chr_re, posi, dm1, dm_op[tid], dm_ops[tid],((rc_i << 1) + un_ii));
posi = x;
*/
if(dm1 < dm_op[tid])
{
#ifdef DM_COPY_SINGLE
for(dm_i = 0; dm_i < v_cnt; dm_i++)
{
ops_vector_pos1[tid][dm_i] = op_vector_pos1[tid][dm_i];
ops_dm_l1[tid][dm_i] = op_dm_l1[tid][dm_i];
ops_dm_r1[tid][dm_i] = op_dm_r1[tid][dm_i];
if(!((op_dm_l1[tid][dm_i] == 0) && (op_dm_r1[tid][dm_i] == 0)))
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars);
ops_rc[tid][dm_i] = op_rc[tid][dm_i];
}
vs_cnt = v_cnt;
dm_ops[tid] = dm_op[tid];
#endif
v_cnt = 0;
op_vector_pos1[tid][v_cnt] = posi;
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
#ifdef ALTER_DEBUG_ANCHOR
seed_length_arr[tid][v_cnt].seed_length = seed_length1;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
op_rc[tid][v_cnt] = ((rc_i << 1) + un_ii);
++v_cnt;
dm_op[tid] = dm1;
}
else if(dm1 == dm_op[tid])
{
if(v_cnt < cus_max_output_ali)
{
op_vector_pos1[tid][v_cnt] = posi;
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
#ifdef ALTER_DEBUG_ANCHOR
seed_length_arr[tid][v_cnt].seed_length = seed_length1;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
op_rc[tid][v_cnt] = ((rc_i << 1) + un_ii);
++v_cnt;
}
}
else if(dm1 < dm_ops[tid])
{
vs_cnt = 0;
ops_vector_pos1[tid][vs_cnt] = posi;
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
ops_rc[tid][vs_cnt] = ((rc_i << 1) + un_ii);
++vs_cnt;
dm_ops[tid] = dm1;
}
else if(dm1 == dm_ops[tid])
{
if(vs_cnt < cus_max_output_ali)
{
ops_vector_pos1[tid][vs_cnt] = posi;
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
ops_rc[tid][vs_cnt] = ((rc_i << 1) + un_ii);
++vs_cnt;
}
}
}
}
}
}
#ifdef PR_SINGLE
if(seed_re_r[tid] == 1)
{
if(min_mis[tid] <= dm_op[tid])
{
if(min_mis[tid] < dm_op[tid])
{
dm_op[tid] = min_mis[tid];
v_cnt = 0;
}
for(rc_i = 0; rc_i < 2; rc_i++)
for(rc_ii = 0; rc_ii < 2; rc_ii++)
for(v_cnt_i = 0; v_cnt_i < seedpos_misn[rc_i][rc_ii][tid]; v_cnt_i++)
{
if(seedpos_mis[rc_i][rc_ii][tid][v_cnt_i] == min_mis[tid])
{
if(v_cnt < cus_max_output_ali)
{
op_vector_pos1[tid][v_cnt] = seedpos[rc_i][rc_ii][tid][v_cnt_i];
op_dm_l1[tid][v_cnt] = 0;
op_dm_r1[tid][v_cnt] = 0;
op_rc[tid][v_cnt] = ((rc_i << 1) + rc_ii);
#ifdef ALTER_DEBUG_ANCHOR
seed_length_arr[tid][v_cnt].seed_length = 0;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
++v_cnt;
}
}
}
}
else if(min_mis[tid] <= dm_ops[tid])
{
if(min_mis[tid] < dm_ops[tid])
{
dm_ops[tid] = min_mis[tid];
vs_cnt = 0;
}
for(rc_i = 0; rc_i < 2; rc_i++)
for(rc_ii = 0; rc_ii < 2; rc_ii++)
for(v_cnt_i = 0; v_cnt_i < seedpos_misn[rc_i][rc_ii][tid]; v_cnt_i++)
{
if(seedpos_mis[rc_i][rc_ii][tid][v_cnt_i] == min_mis[tid])
{
if(vs_cnt < cus_max_output_ali)
{
ops_vector_pos1[tid][vs_cnt] = seedpos[rc_i][rc_ii][tid][v_cnt_i];
ops_dm_l1[tid][vs_cnt] = 0;
ops_dm_r1[tid][vs_cnt] = 0;
ops_rc[tid][vs_cnt] = ((rc_i << 1) + rc_ii);
++vs_cnt;
}
}
}
}
}
#endif
if(v_cnt > 0)
{
#ifdef ALTER_DEBUG_ANCHOR
if(v_cnt > 1) qsort(seed_length_arr[tid], v_cnt, sizeof(seed_length_array), compare_seed_length);
#endif
#ifdef REDUCE_ANCHOR
tra1_i = 0;
tra2_i = 0;
anchor_n1 = 0;
anchor_n2 = 0;
memset(op_mask, 0, v_cnt << 1);
memset(ops_mask, 0, vs_cnt << 1);
for(va_cnt_i = 0; va_cnt_i < v_cnt; va_cnt_i++)
{
#ifdef ALTER_DEBUG_ANCHOR
if(v_cnt > 1) tra_i = seed_length_arr[tid][va_cnt_i].index;
else tra_i = va_cnt_i;
#else
tra_i = va_cnt_i;
#endif
if((op_rc[tid][tra_i] == 0) || (op_rc[tid][tra_i] == 3))
{
poses1[tid][anchor_n1] = op_vector_pos1[tid][tra_i];
ls1[tid][anchor_n1] = op_dm_l1[tid][tra_i];
rs1[tid][anchor_n1] = op_dm_r1[tid][tra_i];
rcs1[tid][anchor_n1] = op_rc[tid][tra_i];
dms1[tid][anchor_n1] = dm_op[tid];
orders1[tid][anchor_n1] = tra_i;
anchor_n1++;
}
else
{
poses2[tid][anchor_n2] = op_vector_pos1[tid][tra_i];
ls2[tid][anchor_n2] = op_dm_l1[tid][tra_i];
rs2[tid][anchor_n2] = op_dm_r1[tid][tra_i];
rcs2[tid][anchor_n2] = op_rc[tid][tra_i];
dms2[tid][anchor_n2] = dm_op[tid];
orders2[tid][anchor_n2] = tra_i;
anchor_n2++;
}
}
for(tra_i = 0; tra_i < vs_cnt; tra_i++)
{
if((ops_rc[tid][tra_i] == 0) || (ops_rc[tid][tra_i] == 3))
{
poses1[tid][anchor_n1] = ops_vector_pos1[tid][tra_i];
ls1[tid][anchor_n1] = ops_dm_l1[tid][tra_i];
rs1[tid][anchor_n1] = ops_dm_r1[tid][tra_i];
rcs1[tid][anchor_n1] = ops_rc[tid][tra_i];
dms1[tid][anchor_n1] = dm_ops[tid];
orders1[tid][anchor_n1] = tra_i + MAX_REDUCE_ANCHOR_NUM;
anchor_n1++;
}
else
{
poses2[tid][anchor_n2] = ops_vector_pos1[tid][tra_i];
ls2[tid][anchor_n2] = ops_dm_l1[tid][tra_i];
rs2[tid][anchor_n2] = ops_dm_r1[tid][tra_i];
rcs2[tid][anchor_n2] = ops_rc[tid][tra_i];
dms2[tid][anchor_n2] = dm_ops[tid];
orders2[tid][anchor_n2] = tra_i + MAX_REDUCE_ANCHOR_NUM;
anchor_n2++;
}
}
#endif
#ifdef ANCHOR_HASH_ALI
for(anchor_hash_i = 0; anchor_hash_i < 4; anchor_hash_i++)
{
if(anchor_hash_i == 0)
{
read_length = read_length2;
ori = read_bit2[tid][1];
}
else if(anchor_hash_i == 1)
{
read_length = read_length1;
ori = read_bit1[tid][0];
}
else if(anchor_hash_i == 2)
{
read_length = read_length1;
ori = read_bit1[tid][1];
}
else
{
read_length = read_length2;
ori = read_bit2[tid][0];
}
des_i = 0;
for(ori_i = 0; ori_i < read_length >> 5; ori_i++)
{
for(char_i = 0; (char_i <= 64 - k_anchor_b) && (des_i <= read_length - k_anchor); char_i += 2, des_i++)
{
rh[tid][des_i].des = ((ori[ori_i] >> (64 - char_i - k_anchor_b)) & anchor_mask);
rh[tid][des_i].off_set = des_i;
}
//note that boundary value
for(char_i = 2; (char_i < k_anchor_b) && (des_i <= read_length - k_anchor); char_i += 2, des_i++)
{
rh[tid][des_i].des = ((ori[ori_i] & anchor_mask_boundary_re[char_i >> 1]) << char_i) | (ori[ori_i + 1] >> (64 - char_i));// & anchor_mask_boundary[char_i >> 1]
rh[tid][des_i].off_set = des_i;
}
}
qsort(rh[tid], des_i, sizeof(read_h), compare_read_hash);
memset(anchor_hash[tid][anchor_hash_i], 0, 1 << 17);
read_k_p = rh[tid][0].des;
anchor_hash[tid][anchor_hash_i][read_k_p >> k_anchor_back] = 0;
anchor_array[tid][anchor_hash_i][0] = (read_k_p & anchor_back_mask);
anchor_point[tid][anchor_hash_i][0] = 0;
anchor_pos[tid][anchor_hash_i][0] = rh[tid][0].off_set;
array_i = 1;
array_i_p = 0;
for(char_i = 1; char_i < des_i; char_i++)
{
anchor_pos[tid][anchor_hash_i][char_i] = rh[tid][char_i].off_set;
read_k_t = rh[tid][char_i].des;
if((read_k_t >> k_anchor_back) == (read_k_p >> k_anchor_back))
{
if((read_k_t & anchor_back_mask) != (read_k_p & anchor_back_mask))
{
anchor_array[tid][anchor_hash_i][array_i] = (read_k_t & anchor_back_mask);
anchor_point[tid][anchor_hash_i][array_i] = char_i;
array_i++;
}
}
else
{
anchor_hash[tid][anchor_hash_i][read_k_t >> k_anchor_back] = (array_i << 5);
anchor_hash[tid][anchor_hash_i][read_k_p >> k_anchor_back] |= (array_i - array_i_p);
array_i_p = array_i;
anchor_array[tid][anchor_hash_i][array_i] = (read_k_t & anchor_back_mask);
anchor_point[tid][anchor_hash_i][array_i] = char_i;
array_i++;
}
read_k_p = read_k_t;
}
anchor_hash[tid][anchor_hash_i][read_k_p >> k_anchor_back] |= (array_i - array_i_p);
anchor_point[tid][anchor_hash_i][array_i] = char_i;
}
#endif
v_cnt_i = 0;
#ifdef ALTER_DEBUG_ANCHOR
if(v_cnt > 1) v_cnt_i = seed_length_arr[tid][v_cnt_i].index;
#endif
#ifdef REDUCE_ANCHOR
op_mask[v_cnt_i] = 1;
#endif
x = op_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re1 = mid;
break;
}
chr_re1 = low;
}
sam_pos1 = op_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re1 - 1] + 1;
#ifdef FIX_SA
op_rc_tmp = op_rc[tid][v_cnt_i];
#endif
if(op_rc[tid][v_cnt_i] == 0)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
ksw_s = x + end_dis1[tid] - devi;
ksw_e = x + insert_dis + devi;
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else if(op_rc[tid][v_cnt_i] == 1)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
ksw_s = x - (end_dis1[tid] + devi);
ksw_e = x - (end_dis1[tid] - devi) + read_length1;
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else if(op_rc[tid][v_cnt_i] == 2)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
ksw_s = x + (end_dis2[tid] - devi);
ksw_e = x + insert_dis + devi;
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
else
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
ksw_s = x - (end_dis2[tid] + devi);
ksw_e = x - (end_dis2[tid] - devi) + read_length2;
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
#ifdef ANCHOR_HASH_ALI
anchor_hash_p = anchor_hash[tid][op_rc[tid][v_cnt_i]];
anchor_array_p = anchor_array[tid][op_rc[tid][v_cnt_i]];
anchor_point_p = anchor_point[tid][op_rc[tid][v_cnt_i]];
anchor_pos_p = anchor_pos[tid][op_rc[tid][v_cnt_i]];
#endif
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = op_dm_l1[tid][v_cnt_i];
s_r_o_r = op_dm_r1[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m_1);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length_1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length_1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length_1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p1 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length_1)
{
sn = sprintf(cigar_p1 + snt, "%uS", read_length_1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p1[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p1[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_1 != cigar_len)
{
if(read_length_1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_1);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m_1);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_1 - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos1 = sam_pos1 + i_n1 - d_n1 + s_offset1;
//use ksw to find the other end alignment
ksw_re = 0;
#ifdef REDUCE_ANCHOR
other_end_flag = 0;
#endif
#ifdef ANCHOR_HASH_ALI
buffer_i = 0;
r_b_v = 0;
for(base_i = ksw_s - 1; base_i < ksw_e - k_anchor; base_i += anchor_seed_d)
{
if(base_i + k_anchor - 1 < r_b_v) continue;
base_re = (base_i & 0X1f);
if(base_re <= k_anchor_re)
{
anchor_ref = ((buffer_ref_seq[base_i >> 5] >> ((k_anchor_re - base_re) << 1)) & anchor_mask);
}
else
{
anchor_ref = (((buffer_ref_seq[base_i >> 5] & anchor_mask_boundary[32 - base_re]) << ((base_re - k_anchor_re) << 1)) | (buffer_ref_seq[(base_i >> 5) + 1] >> ((32 + k_anchor_re - base_re) << 1)));
}
max_right = 0;
for(tra_i = 0; tra_i < (anchor_hash_p[anchor_ref >> 4] & 0X1f); tra_i++)
{
array_index = (anchor_hash_p[anchor_ref >> 4] >> 5) + tra_i;
if(anchor_array_p[array_index] == (anchor_ref & 0Xf))
{
max_seed_length = 0;
for(print_i = anchor_point_p[array_index]; print_i < anchor_point_p[array_index + 1]; print_i++)
{
//extension on both sides
for(left_i = anchor_pos_p[print_i] - 1, base_i_off_l = base_i - 1; (left_i >= 0) && (base_i_off_l >= ksw_s - 1); left_i--, base_i_off_l--)
{
#ifdef CHAR_CP
if(((read_bit_2[tid][left_i >> 5] >> ((31 - (left_i & 0X1f)) << 1)) & 0X3) != ((buffer_ref_seq[base_i_off_l >> 5] >> ((31 - (base_i_off_l & 0X1f)) << 1)) & 0X3))
break;
#else
if(sam_seq2[left_i] != Dna5Tochar[((buffer_ref_seq[base_i_off_l >> 5] >> ((31 - (base_i_off_l & 0X1f)) << 1)) & 0X3)])
break;
#endif
}
for(right_i = anchor_pos_p[print_i] + k_anchor, base_i_off_r = base_i + k_anchor; (right_i < read_length_2) && (base_i_off_r < ksw_e); right_i++, base_i_off_r++)
{
#ifdef CHAR_CP
if(((read_bit_2[tid][right_i >> 5] >> ((31 - (right_i & 0X1f)) << 1)) & 0X3) != ((buffer_ref_seq[base_i_off_r >> 5] >> ((31 - (base_i_off_r & 0X1f)) << 1)) & 0X3))
break;
#else
if(sam_seq2[right_i] != Dna5Tochar[((buffer_ref_seq[base_i_off_r >> 5] >> ((31 - (base_i_off_r & 0X1f)) << 1)) & 0X3)])
break;
#endif
}
seed_length = right_i - left_i - 1;
if(seed_length > max_seed_length)
{
max_seed_length = seed_length;
max_right = base_i_off_r;
}
anchor_seed_buffer[tid][buffer_i].read_left_off = left_i;
anchor_seed_buffer[tid][buffer_i].read_right_off = right_i;
anchor_seed_buffer[tid][buffer_i].ref_left_off = base_i_off_l;
anchor_seed_buffer[tid][buffer_i].ref_right_off = base_i_off_r;
anchor_seed_buffer[tid][buffer_i].seed_length = seed_length;
buffer_i++;
}
break;
}
}
r_b_v = max_right;
}
if((buffer_i > 0) && (max_seed_length > anchor_seed_length_thr))
{
qsort(anchor_seed_buffer[tid], buffer_i, sizeof(anchor_seed), comepare_anchor_seed);
//LV
left_i = anchor_seed_buffer[tid][0].read_left_off;
right_i = anchor_seed_buffer[tid][0].read_right_off;
base_i_off_l = anchor_seed_buffer[tid][0].ref_left_off;
base_i_off_r = anchor_seed_buffer[tid][0].ref_right_off;
d_n1 = 0;
i_n1 = 0;
if((left_i == -1) && (right_i == read_length_2))
{
strcpy(cigar_p2, cigar_m_2);
}
else //indel
{
#ifdef LV_CCIGAR
#ifdef CHAR_CP
for(bit_char_i = left_i, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
//33
for(bit_char_i = base_i_off_l, read_b_i = 0; bit_char_i > base_i_off_l - left_i - 33; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = left_i, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
//33
for(bit_char_i = base_i_off_l, read_b_i = 0; bit_char_i > base_i_off_l - left_i - 33; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
dm_l2 = computeEditDistanceWithCigar_s_nm_left(ali_ref_seq[tid], left_i + 33, read_char[tid], left_i + 1, lv_k_2, cigarBuf1, f_cigarn, L[tid], &nm_score1, &s_offset2);//, 0
#ifdef CHAR_CP
for(bit_char_i = right_i, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = base_i_off_r, read_b_i = 0; bit_char_i < base_i_off_r + read_length_2 - right_i + 32; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = right_i, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for(bit_char_i = base_i_off_r, read_b_i = 0; bit_char_i < base_i_off_r + read_length_2 - right_i + 32; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
dm_r2 = computeEditDistanceWithCigar_s_nm(ali_ref_seq[tid], read_length_2 - right_i + 32, read_char[tid], read_length_2 - right_i, lv_k_2, cigarBuf2, f_cigarn, L[tid], &nm_score2);//, 0
#endif
//deal with cigar of LV
//deal with front and back lv cigar
m_m_n = anchor_seed_buffer[tid][0].seed_length;
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok (cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
if((left_i != -1) && (right_i != read_length_2))
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if(left_i == -1)
{
if(b_cigar[pchl] == 'M')
sn = sprintf(cigar_p2, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
else sn = sprintf(cigar_p2, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
else
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
#ifdef CIGAR_LEN_ERR
#ifdef FIX_SA
sv_s_len_p = 0;
#endif
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
#ifdef FIX_SA
if(cigar_p2[s_o_tmp - 1] == 'S')
sv_s_len_p += cigar_len_tmp;
#endif
if(cigar_p2[s_o_tmp - 1] == 'I')
dm_l2 += cigar_len_tmp;
}else{
cigar_len_tmp = atoi(pch_tmp);
dm_l2 += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_2 != cigar_len)
{
if(read_length_2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m_2);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset2 = 0;
#endif
sam_pos2 = base_i_off_l - left_i + i_n1 - d_n1 - chr_end_n[chr_re1 - 1] + 2 + s_offset2;
chr_re2 = chr_re1;
ksw_re = 1;
}
else
{
#ifdef REDUCE_ANCHOR
if((op_rc[tid][v_cnt_i] == 0) || (op_rc[tid][v_cnt_i] == 3))
{
other_end_flag = 0;
while(tra2_i < anchor_n2)
{
rcs = rcs2[tid][tra2_i];
rs = rs2[tid][tra2_i];
ls = ls2[tid][tra2_i];
sam_pos2 = poses2[tid][tra2_i];
dm_l2 = dms2[tid][tra2_i];
dm_r2 = 0;
if(orders2[tid][tra2_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders2[tid][tra2_i] - MAX_REDUCE_ANCHOR_NUM;
if(ops_mask[v_cnt_i_tmp] == 0)
{
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
ops_mask[v_cnt_i_tmp] = 1;
other_end_flag = 1;
tra2_i++;
break;
}
}
else
{
v_cnt_i_tmp = orders2[tid][tra2_i];
if(op_mask[v_cnt_i_tmp] == 0)
{
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
op_mask[v_cnt_i_tmp] = 1;
other_end_flag = 1;
tra2_i++;
break;
}
}
tra2_i++;
}
}
else
{
other_end_flag = 0;
while(tra1_i < anchor_n1)
{
rcs = rcs1[tid][tra1_i];
rs = rs1[tid][tra1_i];
ls = ls1[tid][tra1_i];
sam_pos2 = poses1[tid][tra1_i];
dm_l2 = dms1[tid][tra1_i];
dm_r2 = 0;
if(orders1[tid][tra1_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders1[tid][tra1_i] - MAX_REDUCE_ANCHOR_NUM;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
if(ops_mask[v_cnt_i_tmp] == 1)
{
ops_mask[v_cnt_i_tmp] = 1;
tra1_i++;
other_end_flag = 1;
break;
}
}
else
{
v_cnt_i_tmp = orders1[tid][tra1_i];
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
if(op_mask[v_cnt_i_tmp] == 1)
{
op_mask[v_cnt_i_tmp] = 1;
tra1_i++;
other_end_flag = 1;
break;
}
}
tra1_i++;
}
}
if(other_end_flag)
{
x = sam_pos2;
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re2 = mid;
break;
}
chr_re2 = low;
}
sam_pos2 = x - chr_end_n[chr_re2 - 1] + 1;
if(rcs == 0)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
/*
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else if(rcs == 1)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else if(rcs == 2)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
/*
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
else
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = ls;
s_r_o_r = rs;
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m_2);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length_1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length_1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length_1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length_1)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length_1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p2[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
#ifdef FIX_SA
sv_s_len_p = 0;
#endif
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
#ifdef FIX_SA
if(cigar_p2[s_o_tmp - 1] == 'S')
sv_s_len_p += cigar_len_tmp;
#endif
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_1 != cigar_len)
{
if(read_length_1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_1);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m_1);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_1 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos2 = sam_pos2 + i_n1 - d_n1 + s_offset1;
ksw_re = 1;
}
else
{
sam_pos2 = sam_pos1;
#ifdef PICARD_BUG
strcpy(cigar_p2, cigar_p1);
#else
strcpy(cigar_p2, "*");
#endif
chr_re2 = chr_re1;
ksw_re = 0;
}
#else
sam_pos2 = sam_pos1;
#ifdef PICARD_BUG
strcpy(cigar_p2, cigar_p1);
#else
strcpy(cigar_p2, "*");
#endif
chr_re2 = chr_re1;
ksw_re = 0;
#endif
}
#endif
if(op_rc[tid][v_cnt_i] == 0)
{
#ifdef FIX_SV
sv_add = 2;
#endif
#ifdef CHAR_CP
strcpy(sam_seq1, seqio[seqi].read_seq1);
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 2)
strcpy(sam_seq2, seqio[seqi].read_seq2);
else
{
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
}
//if((rcs == 0) || (rcs == 3)) printf("Error: %u\n", rcs);
}
else
{
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
}
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#endif
seq1p = sam_seq1;
if(ksw_re == 1)
{
sam_cross = sam_pos2 + read_length2 - sam_pos1;
if((sam_cross > insert_dis + devi) || (sam_cross < insert_dis - devi) || (chr_re1 != chr_re2))
{
if((other_end_flag) && (rcs == 2))
{
sam_flag1 = 65;
sam_flag2 = 129;
}
else
{
sam_flag1 = 97;
sam_flag2 = 145;
}
}
else
{
if((other_end_flag) && (rcs == 2))
{
sam_flag1 = 67;
sam_flag2 = 131;
}
else
{
sam_flag1 = 99;
sam_flag2 = 147;
}
}
seq2p = sam_seq2;
}
else
{
sam_flag1 = 73;
sam_flag2 = 133;
sam_cross = 0;
seq2p = seqio[seqi].read_seq2;
qual_flag = 2;
#ifdef SAMTOOLS_BUG
sam_pos2 = 0;
chr_re2 = chr_file_n;
#endif
}
cp1 = cigar_p1;
cp2 = cigar_p2;
seqio[seqi].nm1 = dm_op[tid];
seqio[seqi].nm2 = dm_l2 + dm_r2;
}
else if(op_rc[tid][v_cnt_i] == 1)
{
#ifdef FIX_SV
sv_add = 1;
#endif
#ifdef CHAR_CP
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 0)
strcpy(sam_seq2, seqio[seqi].read_seq1);
else
{
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
}
//if((rcs == 1) || (rcs == 2)) printf("Error: %u\n", rcs);
}
else
{
strcpy(sam_seq2, seqio[seqi].read_seq1);
}
#else
strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#endif
seq2p = sam_seq1;
if(ksw_re == 1)
{
chr_re1 = chr_re1 ^ chr_re2;
chr_re2 = chr_re1 ^ chr_re2;
chr_re1 = chr_re1 ^ chr_re2;
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_pos2 = sam_pos1 ^ sam_pos2;
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_cross = sam_pos2 + read_length2 - sam_pos1;
if((sam_cross > insert_dis + devi) || (sam_cross < insert_dis - devi) || (chr_re1 != chr_re2))
{
if((other_end_flag) && (rcs != 0))
{
sam_flag1 = 113;
sam_flag2 = 177;
}
else
{
sam_flag1 = 97;
sam_flag2 = 145;
}
}
else
{
if((other_end_flag) && (rcs != 0))
{
sam_flag1 = 115;
sam_flag2 = 179;
}
else
{
sam_flag1 = 99;
sam_flag2 = 147;
}
}
seq1p = sam_seq2;
}
else
{
sam_flag1 = 117;
sam_flag2 = 153;
sam_cross = 0;
seq1p = seqio[seqi].read_seq1;
qual_flag = 1;
#ifdef SAMTOOLS_BUG
sam_pos2 = sam_pos1;
sam_pos1 = 0;
chr_re2 = chr_re1;
chr_re1 = chr_file_n;
#endif
}
cp1 = cigar_p2;
cp2 = cigar_p1;
seqio[seqi].nm1 = dm_l2 + dm_r2;
seqio[seqi].nm2 = dm_op[tid];
}
else if(op_rc[tid][v_cnt_i] == 2)
{
#ifdef FIX_SV
sv_add = 1;
#endif
#ifdef CHAR_CP
strcpy(sam_seq1, seqio[seqi].read_seq2);
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 0)
strcpy(sam_seq2, seqio[seqi].read_seq1);
else
{
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
}
//if((rcs == 1) || (rcs == 2)) printf("Error: %u\n", rcs);
}
else
{
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
}
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#endif
seq2p = sam_seq1;
if(ksw_re == 1)
{
chr_re1 = chr_re1 ^ chr_re2;
chr_re2 = chr_re1 ^ chr_re2;
chr_re1 = chr_re1 ^ chr_re2;
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_pos2 = sam_pos1 ^ sam_pos2;
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_cross = sam_pos2 - read_length1 - sam_pos1;
if((sam_cross > insert_dis + devi) || (sam_cross < insert_dis - devi) || (chr_re1 != chr_re2))
{
if((other_end_flag) && (rcs == 0))
{
sam_flag1 = 65;
sam_flag2 = 129;
}
else
{
sam_flag1 = 81;
sam_flag2 = 161;
}
}
else
{
if((other_end_flag) && (rcs == 0))
{
sam_flag1 = 67;
sam_flag2 = 131;
}
else
{
sam_flag1 = 83;
sam_flag2 = 163;
}
}
seq1p = sam_seq2;
}
else
{
sam_flag1 = 69;
sam_flag2 = 137;
sam_cross = 0;
seq1p = seqio[seqi].read_seq1;
qual_flag = 1;
#ifdef SAMTOOLS_BUG
sam_pos2 = sam_pos1;
sam_pos1 = 0;
chr_re2 = chr_re1;
chr_re1 = chr_file_n;
#endif
}
cp1 = cigar_p2;
cp2 = cigar_p1;
seqio[seqi].nm1 = dm_l2 + dm_r2;
seqio[seqi].nm2 = dm_op[tid];
}
else
{
#ifdef FIX_SV
sv_add = 2;
#endif
#ifdef CHAR_CP
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 2)
strcpy(sam_seq2, seqio[seqi].read_seq2);
else
{
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
}
//if((rcs == 0) || (rcs == 3)) printf("Error: %u\n", rcs);
}
else
{
strcpy(sam_seq2, seqio[seqi].read_seq2);
}
#else
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#endif
seq1p = sam_seq1;
seq2p = sam_seq2;
if(ksw_re == 1)
{
sam_cross = sam_pos2 - read_length1 - sam_pos1;
if((sam_cross > insert_dis + devi) || (sam_cross < insert_dis - devi) || (chr_re1 != chr_re2))
{
if((other_end_flag) && (rcs != 2))
{
sam_flag1 = 113;
sam_flag2 = 177;
}
else
{
sam_flag1 = 81;
sam_flag2 = 161;
}
}
else
{
if((other_end_flag) && (rcs != 2))
{
sam_flag1 = 115;
sam_flag2 = 179;
}
else
{
sam_flag1 = 83;
sam_flag2 = 163;
}
}
}
else
{
sam_flag1 = 89;
sam_flag2 = 181;
sam_cross = 0;
qual_flag = 2;
#ifdef SAMTOOLS_BUG
sam_pos2 = 0;
chr_re2 = chr_file_n;
#endif
}
cp1 = cigar_p1;
cp2 = cigar_p2;
seqio[seqi].nm1 = dm_op[tid];
seqio[seqi].nm2 = dm_l2 + dm_r2;
}
#ifdef OUTPUT_ARR
seqio[seqi].flag1 = sam_flag1;
seqio[seqi].flag2 = sam_flag2;
//seqio[seqi].chr_re = chr_re;
seqio[seqi].chr_re1 = chr_re1;
seqio[seqi].chr_re2 = chr_re2;
if(sam_pos1 <= 0)
{
sam_pos1 = 1;
}
else
{
if((sam_pos1 + read_length1 - 1) > (chr_end_n[chr_re1] - chr_end_n[chr_re1 - 1]))
sam_pos1 = chr_end_n[chr_re1] - chr_end_n[chr_re1 - 1] - 1 - read_length1;
}
if(sam_pos2 <= 0)
{
sam_pos2 = 1;
}
else
{
if((sam_pos2 + read_length2 - 1) > (chr_end_n[chr_re2] - chr_end_n[chr_re2 - 1]))
sam_pos2 = chr_end_n[chr_re2] - chr_end_n[chr_re2 - 1] - 1 - read_length2;
}
seqio[seqi].pos1 = sam_pos1;
seqio[seqi].pos2 = sam_pos2;
seqio[seqi].cross = sam_cross;
strcpy(pr_cigar1_buffer[seqi], cp1);
seqio[seqi].cigar1 = pr_cigar1_buffer[seqi];
strcpy(pr_cigar2_buffer[seqi], cp2);
seqio[seqi].cigar2 = pr_cigar2_buffer[seqi];
if((sam_flag1 == 99) || (sam_flag1 == 117) || (sam_flag1 == 97))
{
strcpy(read_rev_buffer[seqi], seq2p);
read_rev_buffer[seqi][read_length2] = '\0';
seqio[seqi].seq2 = read_rev_buffer[seqi];
seqio[seqi].seq1 = seqio[seqi].read_seq1;
strrev1(qual2_buffer[seqi]);
}
else if((sam_flag1 == 83) || (sam_flag1 == 89) || (sam_flag1 == 81))
{
strcpy(read_rev_buffer[seqi], seq1p);
read_rev_buffer[seqi][read_length1] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
seqio[seqi].seq2 = seqio[seqi].read_seq2;
strrev1(qual1_buffer[seqi]);
}
else if((sam_flag1 == 113) || (sam_flag1 == 115))
{
strcpy(read_rev_buffer[seqi], seq1p);
read_rev_buffer[seqi][read_length1] = '\0';
strcpy(read_rev_buffer_1[seqi], seq2p);
read_rev_buffer_1[seqi][read_length2] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
seqio[seqi].seq2 = read_rev_buffer_1[seqi];
}
else
{
seqio[seqi].seq1 = seqio[seqi].read_seq1;
seqio[seqi].seq2 = seqio[seqi].read_seq2;
}
#endif
}
lv_re1f = dm_op[tid];
xa_i_1 = 0;
xa_i_2 = 0;
for(va_cnt_i = 1; va_cnt_i < v_cnt; va_cnt_i++)
{
#ifdef ALTER_DEBUG_ANCHOR
v_cnt_i = seed_length_arr[tid][va_cnt_i].index;
#else
v_cnt_i = va_cnt_i;
#endif
#ifdef REDUCE_ANCHOR
if(op_mask[v_cnt_i] == 1) continue;
op_mask[v_cnt_i] = 1;
#endif
x = op_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
if(chr_re)
sam_pos1 = op_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
else
{
sam_pos1 = op_vector_pos1[tid][v_cnt_i];
chr_re = 1;
}
//chr_res[tid][xa_i] = chr_re;
if(op_rc[tid][v_cnt_i] == 0)
{
#ifdef OUPUT_SINGLE_REPEAT
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
ksw_s = x + end_dis1[tid] - devi;
ksw_e = x + insert_dis + devi;
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else if(op_rc[tid][v_cnt_i] == 1)
{
#ifdef OUPUT_SINGLE_REPEAT
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
ksw_s = x - (end_dis1[tid] + devi);
ksw_e = x - (end_dis1[tid] - devi) + read_length1;
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else if(op_rc[tid][v_cnt_i] == 2)
{
#ifdef OUPUT_SINGLE_REPEAT
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
ksw_s = x + (end_dis2[tid] - devi);
ksw_e = x + insert_dis + devi;
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
else
{
#ifdef OUPUT_SINGLE_REPEAT
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
ksw_s = x - (end_dis2[tid] + devi);
ksw_e = x - (end_dis2[tid] - devi) + read_length2;
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
#ifdef ANCHOR_HASH_ALI
anchor_hash_p = anchor_hash[tid][op_rc[tid][v_cnt_i]];
anchor_array_p = anchor_array[tid][op_rc[tid][v_cnt_i]];
anchor_point_p = anchor_point[tid][op_rc[tid][v_cnt_i]];
anchor_pos_p = anchor_pos[tid][op_rc[tid][v_cnt_i]];
#endif
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = op_dm_l1[tid][v_cnt_i];
s_r_o_r = op_dm_r1[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m_1);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length_1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length_1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length_1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p1 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length_1)
{
sn = sprintf(cigar_p1 + snt, "%uS", read_length_1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p1[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p1[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_1 != cigar_len)
{
if(read_length_1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_1);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m_1);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_1 - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos1 = sam_pos1 + i_n1 - d_n1 + s_offset1;
ksw_re = 0;
#ifdef REDUCE_ANCHOR
other_end_flag = 0;
#endif
#ifdef ANCHOR_HASH_ALI
buffer_i = 0;
r_b_v = 0;
for(base_i = ksw_s - 1; base_i < ksw_e - k_anchor; base_i += anchor_seed_d)
{
if(base_i + k_anchor - 1 < r_b_v) continue;
base_re = (base_i & 0X1f);
if(base_re <= k_anchor_re)
{
anchor_ref = ((buffer_ref_seq[base_i >> 5] >> ((k_anchor_re - base_re) << 1)) & anchor_mask);
}
else
{
anchor_ref = (((buffer_ref_seq[base_i >> 5] & anchor_mask_boundary[32 - base_re]) << ((base_re - k_anchor_re) << 1)) | (buffer_ref_seq[(base_i >> 5) + 1] >> ((32 + k_anchor_re - base_re) << 1)));
}
max_right = 0;
for(tra_i = 0; tra_i < (anchor_hash_p[anchor_ref >> 4] & 0X1f); tra_i++)
{
array_index = (anchor_hash_p[anchor_ref >> 4] >> 5) + tra_i;
if(anchor_array_p[array_index] == (anchor_ref & 0Xf))
{
max_seed_length = 0;
for(print_i = anchor_point_p[array_index]; print_i < anchor_point_p[array_index + 1]; print_i++)
{
//extension on both sides
for(left_i = anchor_pos_p[print_i] - 1, base_i_off_l = base_i - 1; (left_i >= 0) && (base_i_off_l >= ksw_s - 1); left_i--, base_i_off_l--)
{
#ifdef CHAR_CP
if(((read_bit_2[tid][left_i >> 5] >> ((31 - (left_i & 0X1f)) << 1)) & 0X3) != ((buffer_ref_seq[base_i_off_l >> 5] >> ((31 - (base_i_off_l & 0X1f)) << 1)) & 0X3))
break;
#else
if(sam_seq2[left_i] != Dna5Tochar[((buffer_ref_seq[base_i_off_l >> 5] >> ((31 - (base_i_off_l & 0X1f)) << 1)) & 0X3)])
break;
#endif
}
for(right_i = anchor_pos_p[print_i] + k_anchor, base_i_off_r = base_i + k_anchor; (right_i < read_length_2) && (base_i_off_r < ksw_e); right_i++, base_i_off_r++)
{
#ifdef CHAR_CP
if(((read_bit_2[tid][right_i >> 5] >> ((31 - (right_i & 0X1f)) << 1)) & 0X3) != ((buffer_ref_seq[base_i_off_r >> 5] >> ((31 - (base_i_off_r & 0X1f)) << 1)) & 0X3))
break;
#else
if(sam_seq2[right_i] != Dna5Tochar[((buffer_ref_seq[base_i_off_r >> 5] >> ((31 - (base_i_off_r & 0X1f)) << 1)) & 0X3)])
break;
#endif
}
seed_length = right_i - left_i - 1;
if(seed_length > max_seed_length)
{
max_seed_length = seed_length;
max_right = base_i_off_r;
}
anchor_seed_buffer[tid][buffer_i].read_left_off = left_i;
anchor_seed_buffer[tid][buffer_i].read_right_off = right_i;
anchor_seed_buffer[tid][buffer_i].ref_left_off = base_i_off_l;
anchor_seed_buffer[tid][buffer_i].ref_right_off = base_i_off_r;
anchor_seed_buffer[tid][buffer_i].seed_length = seed_length;
buffer_i++;
}
break;
}
}
r_b_v = max_right;
}
if((buffer_i > 0) && (max_seed_length > anchor_seed_length_thr))
{
qsort(anchor_seed_buffer[tid], buffer_i, sizeof(anchor_seed), comepare_anchor_seed);
//LV
left_i = anchor_seed_buffer[tid][0].read_left_off;
right_i = anchor_seed_buffer[tid][0].read_right_off;
base_i_off_l = anchor_seed_buffer[tid][0].ref_left_off;
base_i_off_r = anchor_seed_buffer[tid][0].ref_right_off;
d_n1 = 0;
i_n1 = 0;
if((left_i == -1) && (right_i == read_length_2))
{
strcpy(cigar_p2, cigar_m_2);
}
else //indel
{
#ifdef LV_CCIGAR
#ifdef CHAR_CP
for(bit_char_i = left_i, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = base_i_off_l, read_b_i = 0; bit_char_i > base_i_off_l - left_i - 33; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = left_i, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for(bit_char_i = base_i_off_l, read_b_i = 0; bit_char_i > base_i_off_l - left_i - 33; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
dm1 = computeEditDistanceWithCigar_s_left(ali_ref_seq[tid], left_i + 33, read_char[tid], left_i + 1, lv_k_2, cigarBuf1, f_cigarn, L[tid], &s_offset2);//, 0
#ifdef CHAR_CP
for(bit_char_i = right_i, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = base_i_off_r, read_b_i = 0; bit_char_i < base_i_off_r + read_length_2 - right_i + 32; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = right_i, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for(bit_char_i = base_i_off_r, read_b_i = 0; bit_char_i < base_i_off_r + read_length_2 - right_i + 32; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
dm2 = computeEditDistanceWithCigar_s(ali_ref_seq[tid], read_length_2 - right_i + 32, read_char[tid], read_length_2 - right_i, lv_k_2, cigarBuf2, f_cigarn, L[tid]);//, 0
#endif
//deal with cigar of LV
//deal with front and back lv cigar
m_m_n = anchor_seed_buffer[tid][0].seed_length;
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok (cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
if((left_i != -1) && (right_i != read_length_2))
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if(left_i == -1)
{
if(b_cigar[pchl] == 'M')
sn = sprintf(cigar_p2, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
else sn = sprintf(cigar_p2, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
else
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_2 != cigar_len)
{
if(read_length_2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m_2);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset2 = 0;
#endif
sam_pos2 = base_i_off_l - left_i + i_n1 - d_n1 - chr_end_n[chr_re - 1] + 2 + s_offset2;
ksw_re = 1;
lv_re2f = dm1 + dm2;
}
else
{
#ifdef REDUCE_ANCHOR
if((op_rc[tid][v_cnt_i] == 0) || (op_rc[tid][v_cnt_i] == 3))
{
other_end_flag = 0;
while(tra2_i < anchor_n2)
{
rcs = rcs2[tid][tra2_i];
rs = rs2[tid][tra2_i];
ls = ls2[tid][tra2_i];
sam_pos2 = poses2[tid][tra2_i];
lv_re2f = dms2[tid][tra2_i];
if(orders2[tid][tra2_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders2[tid][tra2_i] - MAX_REDUCE_ANCHOR_NUM;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
if(ops_mask[v_cnt_i_tmp] == 0)
{
ops_mask[v_cnt_i_tmp] = 1;
other_end_flag = 1;
tra2_i++;
break;
}
}
else
{
v_cnt_i_tmp = orders2[tid][tra2_i];
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
if(op_mask[v_cnt_i_tmp] == 0)
{
op_mask[v_cnt_i_tmp] = 1;
other_end_flag = 1;
tra2_i++;
break;
}
}
tra2_i++;
}
}
else
{
other_end_flag = 0;
while(tra1_i < anchor_n1)
{
rcs = rcs1[tid][tra1_i];
rs = rs1[tid][tra1_i];
ls = ls1[tid][tra1_i];
sam_pos2 = poses1[tid][tra1_i];
lv_re2f = dms1[tid][tra1_i];
if(orders1[tid][tra1_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders1[tid][tra1_i] - MAX_REDUCE_ANCHOR_NUM;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
if(ops_mask[v_cnt_i_tmp] == 0)
{
ops_mask[v_cnt_i_tmp] = 1;
tra1_i++;
other_end_flag = 1;
break;
}
}
else
{
v_cnt_i_tmp = orders1[tid][tra1_i];
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
if(op_mask[v_cnt_i_tmp] == 0)
{
op_mask[v_cnt_i_tmp] = 1;
tra1_i++;
other_end_flag = 1;
break;
}
}
tra1_i++;
}
}
if(other_end_flag)
{
x = sam_pos2;
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos2 = x - chr_end_n[chr_re - 1] + 1;
if(rcs == 0)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
/*
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else if(rcs == 1)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else if(rcs == 2)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
/*
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
else
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = ls;
s_r_o_r = rs;
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m_2);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length_1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length_1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length_1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length_1)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length_1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p2[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_1 != cigar_len)
{
if(read_length_1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_1);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m_1);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_1 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos2 = sam_pos2 + i_n1 - d_n1 + s_offset1;
ksw_re = 1;
}
else
{
sam_pos2 = sam_pos1;
#ifdef PICARD_BUG
strcpy(cigar_p2, cigar_p1);
#else
strcpy(cigar_p2, "*");
#endif
ksw_re = 0;
lv_re2f = 0;
}
#else
sam_pos2 = sam_pos1;
#ifdef PICARD_BUG
strcpy(cigar_p2, cigar_p1);
#else
strcpy(cigar_p2, "*");
#endif
ksw_re = 0;
lv_re2f = 0;
#endif
}
#endif
if(op_rc[tid][v_cnt_i] == 0)
{
cp1 = cigar_p1;
cp2 = cigar_p2;
xa_d1s[tid][xa_i_1] = '+';
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 2) xa_d2s[tid][xa_i_2] = '+';
else xa_d2s[tid][xa_i_2] = '-';
}
else xa_d2s[tid][xa_i_2] = '-';
#else
xa_d2s[tid][xa_i_2] = '-';
#endif
lv_re1b = lv_re1f;
lv_re2b = lv_re2f;
}
else if(op_rc[tid][v_cnt_i] == 1)
{
if(ksw_re == 1)
{
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_pos2 = sam_pos1 ^ sam_pos2;
sam_pos1 = sam_pos1 ^ sam_pos2;
}
cp1 = cigar_p2;
cp2 = cigar_p1;
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 0) xa_d1s[tid][xa_i_1] = '+';
else xa_d1s[tid][xa_i_1] = '-';
}
else xa_d1s[tid][xa_i_1] = '+';
#else
xa_d1s[tid][xa_i_1] = '+';
#endif
xa_d2s[tid][xa_i_2] = '-';
lv_re1b = lv_re2f;
lv_re2b = lv_re1f;
}
else if(op_rc[tid][v_cnt_i] == 2)
{
if(ksw_re == 1)
{
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_pos2 = sam_pos1 ^ sam_pos2;
sam_pos1 = sam_pos1 ^ sam_pos2;
}
cp1 = cigar_p2;
cp2 = cigar_p1;
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 0) xa_d1s[tid][xa_i_1] = '+';
else xa_d1s[tid][xa_i_1] = '-';
}
else xa_d1s[tid][xa_i_1] = '-';
#else
xa_d1s[tid][xa_i_1] = '-';
#endif
xa_d2s[tid][xa_i_2] = '+';
lv_re1b = lv_re2f;
lv_re2b = lv_re1f;
}
else
{
cp1 = cigar_p1;
cp2 = cigar_p2;
xa_d1s[tid][xa_i_1] = '-';
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 2) xa_d2s[tid][xa_i_2] = '+';
else xa_d2s[tid][xa_i_2] = '-';
}
else xa_d2s[tid][xa_i_2] = '+';
#else
xa_d2s[tid][xa_i_2] = '+';
#endif
lv_re1b = lv_re1f;
lv_re2b = lv_re2f;
}
if(sam_pos1 <= 0) sam_pos1 = 1;
if(sam_pos2 <= 0) sam_pos2 = 1;
/*
if((sam_flag1 == 117) || (sam_flag1 == 69))
{
#ifdef PICARD_BUG
//strcpy(cigar_p1s[tid][xa_i], cp2);
#else
//strcpy(cigar_p1s[tid][xa_i], "*");
#endif
strcpy(cigar_p2s[tid][xa_i_2], cp2);
lv_re2s[tid][xa_i_2] = lv_re2b;
chr_res[tid][xa_i_2] = chr_re;
sam_pos2s[tid][xa_i_2] = (uint32_t )sam_pos2;
xa_i_2++;
}
else if((sam_flag1 == 73) || (sam_flag1 == 89))
{
strcpy(cigar_p1s[tid][xa_i_1], cp1);
lv_re1s[tid][xa_i_1] = lv_re1b;
chr_res[tid][xa_i_1] = chr_re;
sam_pos1s[tid][xa_i_1] = (uint32_t )sam_pos1;
xa_i_1++;
#ifdef PICARD_BUG
//strcpy(cigar_p2s[tid][xa_i], cp1);
#else
//strcpy(cigar_p2s[tid][xa_i], "*");
#endif
}
else
{
strcpy(cigar_p1s[tid][xa_i_1], cp1);
strcpy(cigar_p2s[tid][xa_i_2], cp2);
lv_re1s[tid][xa_i_1] = lv_re1b;
lv_re2s[tid][xa_i_2] = lv_re2b;
chr_res[tid][xa_i_1] = chr_re;
sam_pos1s[tid][xa_i_1] = (uint32_t )sam_pos1;
sam_pos2s[tid][xa_i_2] = (uint32_t )sam_pos2;
xa_i_1++;
xa_i_2++;
}
*/
strcpy(cigar_p1s[tid][xa_i_1], cp1);
strcpy(cigar_p2s[tid][xa_i_2], cp2);
lv_re1s[tid][xa_i_1] = lv_re1b;
lv_re2s[tid][xa_i_2] = lv_re2b;
chr_res[tid][xa_i_1] = chr_re;
sam_pos1s[tid][xa_i_1] = (uint32_t )sam_pos1;
sam_pos2s[tid][xa_i_2] = (uint32_t )sam_pos2;
xa_i_1++;
xa_i_2++;
}
lv_re1f = dm_ops[tid];
#ifdef ALT_ALL
#ifdef ALL_ALL_SINGLE
for(v_cnt_i = 0; v_cnt_i < vs_cnt; v_cnt_i++)
#else
for(v_cnt_i = 0; (v_cnt_i < vs_cnt) && (dm_op[tid] + 3 > dm_ops[tid]); v_cnt_i++)
#endif
#else
for(v_cnt_i = 0; (v_cnt_i < vs_cnt) && (v_cnt < 2) && (dm_op[tid] + 3 > dm_ops[tid]); v_cnt_i++)
#endif
{
#ifdef REDUCE_ANCHOR
if(ops_mask[v_cnt_i] == 1) continue;
ops_mask[v_cnt_i] = 1;
#endif
x = ops_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
if(chr_re)
sam_pos1 = ops_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
else
{
sam_pos1 = ops_vector_pos1[tid][v_cnt_i];
chr_re = 1;
}
//chr_res[tid][xa_i] = chr_re;
if(ops_rc[tid][v_cnt_i] == 0)
{
#ifdef OUPUT_SINGLE_REPEAT2
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
ksw_s = x + end_dis1[tid] - devi;
ksw_e = x + insert_dis + devi;
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else if(ops_rc[tid][v_cnt_i] == 1)
{
#ifdef OUPUT_SINGLE_REPEAT2
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
ksw_s = x - (end_dis1[tid] + devi);
ksw_e = x - (end_dis1[tid] - devi) + read_length1;
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else if(ops_rc[tid][v_cnt_i] == 2)
{
#ifdef OUPUT_SINGLE_REPEAT2
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
ksw_s = x + (end_dis2[tid] - devi);
ksw_e = x + insert_dis + devi;
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
else
{
#ifdef OUPUT_SINGLE_REPEAT2
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
ksw_s = x - (end_dis2[tid] + devi);
ksw_e = x - (end_dis2[tid] - devi) + read_length2;
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
#ifdef ANCHOR_HASH_ALI
anchor_hash_p = anchor_hash[tid][ops_rc[tid][v_cnt_i]];
anchor_array_p = anchor_array[tid][ops_rc[tid][v_cnt_i]];
anchor_point_p = anchor_point[tid][ops_rc[tid][v_cnt_i]];
anchor_pos_p = anchor_pos[tid][ops_rc[tid][v_cnt_i]];
#endif
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = ops_dm_l1[tid][v_cnt_i];
s_r_o_r = ops_dm_r1[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m_1);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length_1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length_1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length_1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p1 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length_1)
{
sn = sprintf(cigar_p1 + snt, "%uS", read_length_1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p1[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 +sn;
}
else if(cigar_p1[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_1 != cigar_len)
{
if(read_length_1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_1);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m_1);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_1 - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos1 = sam_pos1 + i_n1 - d_n1 + s_offset1;
ksw_re = 0;
#ifdef REDUCE_ANCHOR
other_end_flag = 0;
#endif
#ifdef ANCHOR_HASH_ALI
buffer_i = 0;
r_b_v = 0;
for(base_i = ksw_s - 1; base_i < ksw_e - k_anchor; base_i += anchor_seed_d)
{
if(base_i + k_anchor - 1 < r_b_v) continue;
base_re = (base_i & 0X1f);
if(base_re <= k_anchor_re)
{
anchor_ref = ((buffer_ref_seq[base_i >> 5] >> ((k_anchor_re - base_re) << 1)) & anchor_mask);
}
else
{
anchor_ref = (((buffer_ref_seq[base_i >> 5] & anchor_mask_boundary[32 - base_re]) << ((base_re - k_anchor_re) << 1)) | (buffer_ref_seq[(base_i >> 5) + 1] >> ((32 + k_anchor_re - base_re) << 1)));
}
max_right = 0;
for(tra_i = 0; tra_i < (anchor_hash_p[anchor_ref >> 4] & 0X1f); tra_i++)
{
array_index = (anchor_hash_p[anchor_ref >> 4] >> 5) + tra_i;
if(anchor_array_p[array_index] == (anchor_ref & 0Xf))
{
max_seed_length = 0;
for(print_i = anchor_point_p[array_index]; print_i < anchor_point_p[array_index + 1]; print_i++)
{
//extension on both sides
for(left_i = anchor_pos_p[print_i] - 1, base_i_off_l = base_i - 1; (left_i >= 0) && (base_i_off_l >= ksw_s - 1); left_i--, base_i_off_l--)
{
#ifdef CHAR_CP
if(((read_bit_2[tid][left_i >> 5] >> ((31 - (left_i & 0X1f)) << 1)) & 0X3) != ((buffer_ref_seq[base_i_off_l >> 5] >> ((31 - (base_i_off_l & 0X1f)) << 1)) & 0X3))
break;
#else
if(sam_seq2[left_i] != Dna5Tochar[((buffer_ref_seq[base_i_off_l >> 5] >> ((31 - (base_i_off_l & 0X1f)) << 1)) & 0X3)])
break;
#endif
}
for(right_i = anchor_pos_p[print_i] + k_anchor, base_i_off_r = base_i + k_anchor; (right_i < read_length_2) && (base_i_off_r < ksw_e); right_i++, base_i_off_r++)
{
#ifdef CHAR_CP
if(((read_bit_2[tid][right_i >> 5] >> ((31 - (right_i & 0X1f)) << 1)) & 0X3) != ((buffer_ref_seq[base_i_off_r >> 5] >> ((31 - (base_i_off_r & 0X1f)) << 1)) & 0X3))
break;
#else
if(sam_seq2[right_i] != Dna5Tochar[((buffer_ref_seq[base_i_off_r >> 5] >> ((31 - (base_i_off_r & 0X1f)) << 1)) & 0X3)])
break;
#endif
}
seed_length = right_i - left_i - 1;
if(seed_length > max_seed_length)
{
max_seed_length = seed_length;
max_right = base_i_off_r;
}
anchor_seed_buffer[tid][buffer_i].read_left_off = left_i;
anchor_seed_buffer[tid][buffer_i].read_right_off = right_i;
anchor_seed_buffer[tid][buffer_i].ref_left_off = base_i_off_l;
anchor_seed_buffer[tid][buffer_i].ref_right_off = base_i_off_r;
anchor_seed_buffer[tid][buffer_i].seed_length = seed_length;
buffer_i++;
}
break;
}
}
r_b_v = max_right;
}
if((buffer_i > 0) && (max_seed_length > anchor_seed_length_thr))
{
qsort(anchor_seed_buffer[tid], buffer_i, sizeof(anchor_seed), comepare_anchor_seed);
//LV
left_i = anchor_seed_buffer[tid][0].read_left_off;
right_i = anchor_seed_buffer[tid][0].read_right_off;
base_i_off_l = anchor_seed_buffer[tid][0].ref_left_off;
base_i_off_r = anchor_seed_buffer[tid][0].ref_right_off;
d_n1 = 0;
i_n1 = 0;
if((left_i == -1) && (right_i == read_length_2))
{
strcpy(cigar_p2, cigar_m_2);
}
else //indel
{
#ifdef LV_CCIGAR
#ifdef CHAR_CP
for(bit_char_i = left_i, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = base_i_off_l, read_b_i = 0; bit_char_i > base_i_off_l - left_i - 33; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = left_i, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for(bit_char_i = base_i_off_l, read_b_i = 0; bit_char_i > base_i_off_l - left_i - 33; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
dm1 = computeEditDistanceWithCigar_s_left(ali_ref_seq[tid], left_i + 33, read_char[tid], left_i + 1, lv_k_2, cigarBuf1, f_cigarn, L[tid], &s_offset2);//, 0
#ifdef CHAR_CP
for(bit_char_i = right_i, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = base_i_off_r, read_b_i = 0; bit_char_i < base_i_off_r + read_length_2 - right_i + 32; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = right_i, read_b_i = 0; bit_char_i < read_length_2; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for(bit_char_i = base_i_off_r, read_b_i = 0; bit_char_i < base_i_off_r + read_length_2 - right_i + 32; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((buffer_ref_seq[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
dm2 = computeEditDistanceWithCigar_s(ali_ref_seq[tid], read_length_2 - right_i + 32, read_char[tid], read_length_2 - right_i, lv_k_2, cigarBuf2, f_cigarn, L[tid]);//, 0
#endif
//deal with cigar of LV
//deal with front and back lv cigar
m_m_n = anchor_seed_buffer[tid][0].seed_length;
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok (cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
if((left_i != -1) && (right_i != read_length_2))
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if(left_i == -1)
{
if(b_cigar[pchl] == 'M')
sn = sprintf(cigar_p2, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
else sn = sprintf(cigar_p2, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
else
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_2 != cigar_len)
{
if(read_length_2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m_2);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset2 = 0;
#endif
sam_pos2 = base_i_off_l - left_i + i_n1 - d_n1 - chr_end_n[chr_re - 1] + 2 + s_offset2;
ksw_re = 1;
lv_re2f = dm1 + dm2;
}
else
{
#ifdef REDUCE_ANCHOR
if((ops_rc[tid][v_cnt_i] == 0) || (ops_rc[tid][v_cnt_i] == 3))
{
other_end_flag = 0;
while(tra2_i < anchor_n2)
{
rcs = rcs2[tid][tra2_i];
rs = rs2[tid][tra2_i];
ls = ls2[tid][tra2_i];
sam_pos2 = poses2[tid][tra2_i];
lv_re2f = dms2[tid][tra2_i];
if(orders2[tid][tra2_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders2[tid][tra2_i] - MAX_REDUCE_ANCHOR_NUM;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
if(ops_mask[v_cnt_i_tmp] == 0)
{
ops_mask[v_cnt_i_tmp] = 1;
tra2_i++;
other_end_flag = 1;
break;
}
}
else
{
v_cnt_i_tmp = orders2[tid][tra2_i];
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
if(op_mask[v_cnt_i_tmp] == 0)
{
op_mask[v_cnt_i_tmp] = 1;
tra2_i++;
other_end_flag = 1;
break;
}
}
tra2_i++;
}
}
else
{
other_end_flag = 0;
while(tra1_i < anchor_n1)
{
rcs = rcs1[tid][tra1_i];
rs = rs1[tid][tra1_i];
ls = ls1[tid][tra1_i];
sam_pos2 = poses1[tid][tra1_i];
lv_re2f = dms1[tid][tra1_i];
if(orders1[tid][tra1_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders1[tid][tra1_i] - MAX_REDUCE_ANCHOR_NUM;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
if(ops_mask[v_cnt_i_tmp] == 0)
{
ops_mask[v_cnt_i_tmp] = 1;
tra1_i++;
other_end_flag = 1;
break;
}
}
else
{
v_cnt_i_tmp = orders1[tid][tra1_i];
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
if(op_mask[v_cnt_i_tmp] == 0)
{
op_mask[v_cnt_i_tmp] = 1;
tra1_i++;
other_end_flag = 1;
break;
}
}
tra1_i++;
}
}
if(other_end_flag)
{
x = sam_pos2;
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos2 = x - chr_end_n[chr_re - 1] + 1;
if(rcs == 0)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
/*
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else if(rcs == 1)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else if(rcs == 2)
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
/*
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
cigar_m_1 = cigar_m2[tid];
cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
read_length_1 = read_length2;
read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
else
{
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
cigar_m_1 = cigar_m1[tid];
cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
read_length_1 = read_length1;
read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = ls;
s_r_o_r = rs;
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m_2);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length_1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length_1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length_1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length_1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length_1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length_1)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length_1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p2[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length_1 != cigar_len)
{
if(read_length_1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length_1);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m_1);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length_1 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos2 = sam_pos2 + i_n1 - d_n1 + s_offset1;
ksw_re = 1;
}
else
{
sam_pos2 = sam_pos1;
#ifdef PICARD_BUG
strcpy(cigar_p2, cigar_p1);
#else
strcpy(cigar_p2, "*");
#endif
ksw_re = 0;
lv_re2f = 0;
}
#else
sam_pos2 = sam_pos1;
#ifdef PICARD_BUG
strcpy(cigar_p2, cigar_p1);
#else
strcpy(cigar_p2, "*");
#endif
ksw_re = 0;
lv_re2f = 0;
#endif
}
#endif
if(ops_rc[tid][v_cnt_i] == 0)
{
cp1 = cigar_p1;
cp2 = cigar_p2;
xa_d1s[tid][xa_i_1] = '+';
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 2) xa_d2s[tid][xa_i_2] = '+';
else xa_d2s[tid][xa_i_2] = '-';
}
else xa_d2s[tid][xa_i_2] = '-';
#else
xa_d2s[tid][xa_i_2] = '-';
#endif
lv_re1b = lv_re1f;
lv_re2b = lv_re2f;
}
else if(ops_rc[tid][v_cnt_i] == 1)
{
if(ksw_re == 1)
{
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_pos2 = sam_pos1 ^ sam_pos2;
sam_pos1 = sam_pos1 ^ sam_pos2;
}
cp1 = cigar_p2;
cp2 = cigar_p1;
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 0) xa_d1s[tid][xa_i_1] = '+';
else xa_d1s[tid][xa_i_1] = '-';
}
else xa_d1s[tid][xa_i_1] = '+';
#else
xa_d1s[tid][xa_i_1] = '+';
#endif
xa_d2s[tid][xa_i_2] = '-';
lv_re1b = lv_re2f;
lv_re2b = lv_re1f;
}
else if(ops_rc[tid][v_cnt_i] == 2)
{
if(ksw_re == 1)
{
sam_pos1 = sam_pos1 ^ sam_pos2;
sam_pos2 = sam_pos1 ^ sam_pos2;
sam_pos1 = sam_pos1 ^ sam_pos2;
}
cp1 = cigar_p2;
cp2 = cigar_p1;
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 0) xa_d1s[tid][xa_i_1] = '+';
else xa_d1s[tid][xa_i_1] = '-';
}
else xa_d1s[tid][xa_i_1] = '-';
#else
xa_d1s[tid][xa_i_1] = '-';
#endif
xa_d2s[tid][xa_i_2] = '+';
lv_re1b = lv_re2f;
lv_re2b = lv_re1f;
}
else
{
cp1 = cigar_p1;
cp2 = cigar_p2;
xa_d1s[tid][xa_i_1] = '-';
#ifdef REDUCE_ANCHOR
if(other_end_flag)
{
if(rcs == 2) xa_d2s[tid][xa_i_2] = '+';
else xa_d2s[tid][xa_i_2] = '-';
}
else xa_d2s[tid][xa_i_2] = '+';
#else
xa_d2s[tid][xa_i_2] = '+';
#endif
lv_re1b = lv_re1f;
lv_re2b = lv_re2f;
}
if(sam_pos1 <= 0) sam_pos1 = 1;
if(sam_pos2 <= 0) sam_pos2 = 1;
/*
if((sam_flag1 == 117) || (sam_flag1 == 69))
{
#ifdef PICARD_BUG
//strcpy(cigar_p1s[tid][xa_i], cp2);
#else
//strcpy(cigar_p1s[tid][xa_i], "*");
#endif
strcpy(cigar_p2s[tid][xa_i_2], cp2);
lv_re2s[tid][xa_i_2] = lv_re2b;
chr_res[tid][xa_i_2] = chr_re;
sam_pos2s[tid][xa_i_2] = (uint32_t )sam_pos2;
xa_i_2++;
}
else if((sam_flag1 == 73) || (sam_flag1 == 89))
{
strcpy(cigar_p1s[tid][xa_i_1], cp1);
lv_re1s[tid][xa_i_1] = lv_re1b;
chr_res[tid][xa_i_1] = chr_re;
sam_pos1s[tid][xa_i_1] = (uint32_t )sam_pos1;
xa_i_1++;
#ifdef PICARD_BUG
//strcpy(cigar_p2s[tid][xa_i], cp1);
#else
//strcpy(cigar_p2s[tid][xa_i], "*");
#endif
}
else
{
strcpy(cigar_p1s[tid][xa_i_1], cp1);
strcpy(cigar_p2s[tid][xa_i_2], cp2);
lv_re1s[tid][xa_i_1] = lv_re1b;
lv_re2s[tid][xa_i_2] = lv_re2b;
chr_res[tid][xa_i_1] = chr_re;
sam_pos1s[tid][xa_i_1] = (uint32_t )sam_pos1;
sam_pos2s[tid][xa_i_2] = (uint32_t )sam_pos2;
xa_i_1++;
xa_i_2++;
}
*/
strcpy(cigar_p1s[tid][xa_i_1], cp1);
strcpy(cigar_p2s[tid][xa_i_2], cp2);
lv_re1s[tid][xa_i_1] = lv_re1b;
lv_re2s[tid][xa_i_2] = lv_re2b;
chr_res[tid][xa_i_1] = chr_re;
sam_pos1s[tid][xa_i_1] = (uint32_t )sam_pos1;
sam_pos2s[tid][xa_i_2] = (uint32_t )sam_pos2;
xa_i_1++;
xa_i_2++;
}
#else
v_cnt = 0;
#endif
seqio[seqi].v_cnt = v_cnt;
if(v_cnt > 0)
{
if(qual_flag == 1)
xa_i_1 = 0;
if(qual_flag == 2)
xa_i_2 = 0;
//seqio[seqi].xa_n = xa_i;
seqio[seqi].xa_n_p1 = xa_i_1;
seqio[seqi].xa_n_p2 = xa_i_2;
seqio[seqi].xa_n1 = 0;
seqio[seqi].xa_n2 = 0;
if((v_cnt == 1) || ((xa_i_1 == 0) && (xa_i_2 == 0)))
{
if(xa_i_1)
seqio[seqi].qualc1 = 20;
else
seqio[seqi].qualc1 = 60;
if(xa_i_2)
seqio[seqi].qualc2 = 20;
else
seqio[seqi].qualc2 = 60;
}
else
{
seqio[seqi].qualc1 = 0;
seqio[seqi].qualc2 = 0;
}
if(qual_flag == 1)
seqio[seqi].qualc1 = 0;
if(qual_flag == 2)
seqio[seqi].qualc2 = 0;
memcpy(chr_res_buffer[seqi], chr_res[tid], (xa_i_1 > xa_i_2 ? xa_i_1:xa_i_2) << 2);
seqio[seqi].chr_res = chr_res_buffer[seqi];
#ifdef FIX_SV
seqio[seqi].xa_n_x1 = 0;
seqio[seqi].xa_n_x2 = 0;
tra_i_n = 0;
if(sv_add == 1)
{
for(tra_i = tra1_i; (tra_i_n < 1) && (tra_i < anchor_n1) && ((xa_i_1 + tra_i_n) < CUS_MAX_OUTPUT_ALI2); tra_i++)
{
if(orders1[tid][tra_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders1[tid][tra_i] - MAX_REDUCE_ANCHOR_NUM;
if(ops_mask[v_cnt_i_tmp] == 1) continue;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
}
else
{
v_cnt_i_tmp = orders1[tid][tra_i];
if(op_mask[v_cnt_i_tmp] == 1) continue;
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
}
sam_pos2 = poses1[tid][tra_i];
x = sam_pos2;
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos2 = x - chr_end_n[chr_re - 1] + 1;
rcs = rcs1[tid][tra_i];
rs = rs1[tid][tra_i];
ls = ls1[tid][tra_i];
chr_res_buffer1[seqi][tra_i_n] = chr_re;
if(rcs == 0)
{
xa_d1s[tid][xa_i_1 + tra_i_n] = '+';
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
/*
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
//cigar_m_1 = cigar_m1[tid];
//cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
//read_length_1 = read_length1;
//read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else
{
xa_d1s[tid][xa_i_1 + tra_i_n] = '-';
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
//cigar_m_1 = cigar_m1[tid];
//cigar_m_2 = cigar_m2[tid];
lv_k_1 = lv_k1;
lv_k_2 = lv_k2;
//read_length_1 = read_length1;
//read_length_2 = read_length2;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_r_o_l = ls;
s_r_o_r = rs;
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m1[tid]);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length1 - s_r_o_l - 1;
}
else//4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
if(str_o[s_o - 1] == 'S') f_cigar[f_cigarn - f_c - 1] = 'S';
else f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length1)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p2[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
#ifdef FIX_SA
sv_s_len = 0;
#endif
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
#ifdef FIX_SA
if(cigar_p2[s_o_tmp - 1] == 'S')
sv_s_len += cigar_len_tmp;
#endif
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length1 != cigar_len)
{
if(read_length1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length1);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m1[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length1 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos2 = sam_pos2 + i_n1 - d_n1 + s_offset1;
if(sam_pos2 == seqio[seqi].pos1) continue;
if(sam_pos2 <= 0) sam_pos2 = 1;
if(sv_s_len_p > sv_s_len)
{
chr_res_buffer1[seqi][tra_i_n] = seqio[seqi].chr_re1;
seqio[seqi].chr_re1 = chr_re;
sam_pos1s[tid][xa_i_1 + tra_i_n] = seqio[seqi].pos1;
if((sam_pos2 + read_length1 - 1) > (chr_end_n[chr_re] - chr_end_n[chr_re - 1]))
sam_pos2 = chr_end_n[chr_re] - chr_end_n[chr_re - 1] - 1 - read_length1;
seqio[seqi].pos1 = sam_pos2;
lv_re1s[tid][xa_i_1 + tra_i_n] = seqio[seqi].nm1;
seqio[seqi].nm1 = dms1[tid][tra_i];
if(seqio[seqi].flag1 & 0X10)
xa_d1s[tid][xa_i_1 + tra_i_n] = '-';
else xa_d1s[tid][xa_i_1 + tra_i_n] = '+';
if(rcs == 0)
{
if(op_rc_tmp == 1) //1+ 2-
{
seqio[seqi].flag1 = 97;
seqio[seqi].flag2 = 145;
//xa_d1s[tid][xa_i_1 + tra_i_n] = '+';
if(seqio[seqi].pos2 > sam_pos2)
sam_cross = seqio[seqi].pos2 + read_length2 - sam_pos2;
else
sam_cross = seqio[seqi].pos2 - sam_pos2 - read_length1;
seqio[seqi].seq1 = seqio[seqi].read_seq1;
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length2] = '\0';
seqio[seqi].seq2 = read_rev_buffer[seqi];
}
else //1+ 2+
{
seqio[seqi].flag1 = 65;
seqio[seqi].flag2 = 129;
//xa_d1s[tid][xa_i_1 + tra_i_n] = '-';
sam_cross = seqio[seqi].pos2 - sam_pos2;
seqio[seqi].seq1 = seqio[seqi].read_seq1;
seqio[seqi].seq2 = seqio[seqi].read_seq2;
//strrev1(qual2_buffer[seqi]);
}
}
else
{
if(op_rc_tmp == 1) //1- 2-
{
seqio[seqi].flag1 = 113;
seqio[seqi].flag2 = 177;
//xa_d1s[tid][xa_i_1 + tra_i_n] = '+';
sam_cross = seqio[seqi].pos2 - sam_pos2;
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length1] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer_1[seqi], sam_seq1);
read_rev_buffer_1[seqi][read_length2] = '\0';
seqio[seqi].seq2 = read_rev_buffer_1[seqi];
//strrev1(qual1_buffer[seqi]);
}
else //1- 2+
{
seqio[seqi].flag1 = 81;
seqio[seqi].flag2 = 161;
//xa_d1s[tid][xa_i_1 + tra_i_n] = '-';
if(sam_pos2 > seqio[seqi].pos2)
sam_cross = seqio[seqi].pos2 - read_length1 - sam_pos2;
else
sam_cross = seqio[seqi].pos2 + read_length2 - sam_pos2;
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length1] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
seqio[seqi].seq2 = seqio[seqi].read_seq2;
}
}
seqio[seqi].cross = sam_cross;
strcpy(cigar_p1s[tid][xa_i_1 + tra_i_n], pr_cigar1_buffer[seqi]);
strcpy(pr_cigar1_buffer[seqi], cigar_p2);
}
else
{
sam_pos1s[tid][xa_i_1 + tra_i_n] = (uint32_t )sam_pos2;
lv_re1s[tid][xa_i_1 + tra_i_n] = dms1[tid][tra_i];
strcpy(cigar_p1s[tid][xa_i_1 + tra_i_n], cigar_p2);
}
tra_i_n++;
}
seqio[seqi].chr_res_s1 = chr_res_buffer1[seqi];
seqio[seqi].xa_n_x1 = tra_i_n;
//xa_i_1 += seqio[seqi].xa_n_x1;
xa_i_1 += tra_i_n;
}
else
{
for(tra_i = tra2_i; (tra_i_n < 1) && (tra_i < anchor_n2) && ((xa_i_2 + tra_i_n) < CUS_MAX_OUTPUT_ALI2); tra_i++)
{
if(orders2[tid][tra_i] >= MAX_REDUCE_ANCHOR_NUM)
{
v_cnt_i_tmp = orders2[tid][tra_i] - MAX_REDUCE_ANCHOR_NUM;
if(ops_mask[v_cnt_i_tmp] == 1) continue;
op_vector_seq1_tmp = ops_vector_seq1[tid][v_cnt_i_tmp];
}
else
{
v_cnt_i_tmp = orders2[tid][tra_i];
if(op_mask[v_cnt_i_tmp] == 1) continue;
op_vector_seq1_tmp = op_vector_seq1[tid][v_cnt_i_tmp];
}
sam_pos2 = poses2[tid][tra_i];
x = sam_pos2;
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos2 = x - chr_end_n[chr_re - 1] + 1;
rcs = rcs2[tid][tra_i];
rs = rs2[tid][tra_i];
ls = ls2[tid][tra_i];
chr_res_buffer2[seqi][tra_i_n] = chr_re;
if(rcs == 1)
{
xa_d2s[tid][xa_i_2 + tra_i_n] = '-';
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][1];
read_bit_2[tid] = read_bit1[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
//strcpy(sam_seq2, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][1];
qual_filt_lv_1_o = qual_filt_lv2[tid][0];
#endif
//cigar_m_1 = cigar_m2[tid];
//cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
//read_length_1 = read_length2;
//read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_reverse;
pound_pos_1_r = pound_pos2_r_reverse;
pound_pos_2_f = pound_pos1_f_forward;
pound_pos_2_r = pound_pos1_r_forward;
}
else
{
xa_d2s[tid][xa_i_2 + tra_i_n] = '+';
#ifdef CHAR_CP
read_bit_1[tid] = read_bit2[tid][0];
read_bit_2[tid] = read_bit1[tid][1];
#else
strcpy(sam_seq1, seqio[seqi].read_seq2);
/*
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
*/
#endif
#ifdef QUAL_FILT_SINGLE_OUT
qual_filt_lv_1 = qual_filt_lv2[tid][0];
qual_filt_lv_1_o = qual_filt_lv2[tid][1];
#endif
//cigar_m_1 = cigar_m2[tid];
//cigar_m_2 = cigar_m1[tid];
lv_k_1 = lv_k2;
lv_k_2 = lv_k1;
//read_length_1 = read_length2;
//read_length_2 = read_length1;
pound_pos_1_f = pound_pos2_f_forward;
pound_pos_1_r = pound_pos2_r_forward;
pound_pos_2_f = pound_pos1_f_reverse;
pound_pos_2_r = pound_pos1_r_reverse;
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_r_o_l = ls;
s_r_o_r = rs;
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m2[tid]);
}
else //indel
{
#ifdef OUTPUT_DEBUG
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length2 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length2;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length2 - s_r_o_l - 1;
}
else//4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_SINGLE_OUT
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length2 - 1- lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k_1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1_tmp[bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k_1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
if(str_o[s_o - 1] == 'S') f_cigar[f_cigarn - f_c - 1] = 'S';
else f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length2)
{
sn = sprintf(cigar_p2 + snt, "%uH", read_length2 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p2[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
#ifdef CIGAR_LEN_ERR
#ifdef FIX_SA
sv_s_len = 0;
#endif
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
#ifdef FIX_SA
if(cigar_p2[s_o_tmp - 1] == 'S')
sv_s_len += cigar_len_tmp;
#endif
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length2 != cigar_len)
{
if(read_length2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m2[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos2 = sam_pos2 + i_n1 - d_n1 + s_offset1;
if(sam_pos2 == seqio[seqi].pos2) continue;
if(sam_pos2 <= 0) sam_pos2 = 1;
if(sv_s_len_p > sv_s_len)
{
chr_res_buffer2[seqi][tra_i_n] = seqio[seqi].chr_re2;
seqio[seqi].chr_re2 = chr_re;
sam_pos2s[tid][xa_i_2 + tra_i_n] = seqio[seqi].pos2;
if((sam_pos2 + read_length2 - 1) > (chr_end_n[chr_re] - chr_end_n[chr_re - 1]))
sam_pos2 = chr_end_n[chr_re] - chr_end_n[chr_re - 1] - 1 - read_length2;
seqio[seqi].pos2 = sam_pos2;
lv_re2s[tid][xa_i_2 + tra_i_n] = seqio[seqi].nm2;
seqio[seqi].nm2 = dms2[tid][tra_i];
if(seqio[seqi].flag2 & 0X10)
xa_d2s[tid][xa_i_1 + tra_i_n] = '-';
else xa_d2s[tid][xa_i_1 + tra_i_n] = '+';
if(op_rc_tmp == 0)
{
if(rcs == 1) //1+ 2-
{
seqio[seqi].flag1 = 97;
seqio[seqi].flag2 = 145;
//xa_d2s[tid][xa_i_2 + tra_i_n] = '-';
if(sam_pos2 > seqio[seqi].pos1)
sam_cross = sam_pos2 + read_length2 - seqio[seqi].pos1;
else
sam_cross = sam_pos2 - seqio[seqi].pos1 - read_length1 ;
seqio[seqi].seq1 = seqio[seqi].read_seq1;
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length2] = '\0';
seqio[seqi].seq2 = read_rev_buffer[seqi];
}
else //1+ 2+
{
seqio[seqi].flag1 = 65;
seqio[seqi].flag2 = 129;
//xa_d2s[tid][xa_i_2 + tra_i_n] = '+';
sam_cross = sam_pos2 - seqio[seqi].pos1;
seqio[seqi].seq1 = seqio[seqi].read_seq1;
seqio[seqi].seq2 = seqio[seqi].read_seq2;
}
}
else
{
if(rcs == 1) //1- 2-
{
seqio[seqi].flag1 = 113;
seqio[seqi].flag2 = 177;
//xa_d2s[tid][xa_i_2 + tra_i_n] = '-';
sam_cross = sam_pos2 - seqio[seqi].pos1;
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length1] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer_1[seqi], sam_seq1);
read_rev_buffer_1[seqi][read_length2] = '\0';
seqio[seqi].seq2 = read_rev_buffer_1[seqi];
}
else //1- 2+
{
seqio[seqi].flag1 = 81;
seqio[seqi].flag2 = 161;
//xa_d2s[tid][xa_i_2 + tra_i_n] = '+';
if(seqio[seqi].pos1 > sam_pos2)
sam_cross = sam_pos2 - read_length1 - seqio[seqi].pos1;
else
sam_cross = sam_pos2 + read_length2 - seqio[seqi].pos1;
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length1] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
seqio[seqi].seq2 = seqio[seqi].read_seq2;
}
}
seqio[seqi].cross = sam_cross;
strcpy(cigar_p2s[tid][xa_i_2 + tra_i_n], pr_cigar2_buffer[seqi]);
strcpy(pr_cigar2_buffer[seqi], cigar_p2);
}
else
{
sam_pos2s[tid][xa_i_2 + tra_i_n] = (uint32_t )sam_pos2;
lv_re2s[tid][xa_i_2 + tra_i_n] = dms2[tid][tra_i];
strcpy(cigar_p2s[tid][xa_i_2 + tra_i_n], cigar_p2);
}
tra_i_n++;
}
seqio[seqi].chr_res_s2 = chr_res_buffer2[seqi];
seqio[seqi].xa_n_x2 = tra_i_n;
//xa_i_2 += seqio[seqi].xa_n_x2;
xa_i_2 += tra_i_n;
}
if(xa_i_1 > 0)
{
memcpy(xa_d1s_buffer[seqi], xa_d1s[tid], xa_i_1);
seqio[seqi].xa_d1s = xa_d1s_buffer[seqi];
memcpy(sam_pos1s_buffer[seqi], sam_pos1s[tid], xa_i_1 << 2);
seqio[seqi].sam_pos1s = sam_pos1s_buffer[seqi];
memcpy(lv_re1s_buffer[seqi], lv_re1s[tid], xa_i_1 << 2);
seqio[seqi].lv_re1s = lv_re1s_buffer[seqi];
for(v_cnt_i = 0; v_cnt_i < xa_i_1; v_cnt_i++)
{
pos_l = strlen(cigar_p1s[tid][v_cnt_i]) + 1;
seqio[seqi].cigar_p1s[v_cnt_i] = (char* )malloc(pos_l);
memcpy(seqio[seqi].cigar_p1s[v_cnt_i], cigar_p1s[tid][v_cnt_i], pos_l);
}
}
if(xa_i_2 > 0)
{
//memcpy(chr_res_buffer[seqi], chr_res[tid], xa_i_2 << 2);
//seqio[seqi].chr_res = chr_res_buffer[seqi];
memcpy(xa_d2s_buffer[seqi], xa_d2s[tid], xa_i_2);
seqio[seqi].xa_d2s = xa_d2s_buffer[seqi];
memcpy(sam_pos2s_buffer[seqi], sam_pos2s[tid], xa_i_2 << 2);
seqio[seqi].sam_pos2s = sam_pos2s_buffer[seqi];
memcpy(lv_re2s_buffer[seqi], lv_re2s[tid], xa_i_2 << 2);
seqio[seqi].lv_re2s = lv_re2s_buffer[seqi];
for(v_cnt_i = 0; v_cnt_i < xa_i_2; v_cnt_i++)
{
pos_l = strlen(cigar_p2s[tid][v_cnt_i]) + 1;
seqio[seqi].cigar_p2s[v_cnt_i] = (char* )malloc(pos_l);
memcpy(seqio[seqi].cigar_p2s[v_cnt_i], cigar_p2s[tid][v_cnt_i], pos_l);
}
}
#else
if(xa_i_1 > 0)
{
memcpy(xa_d1s_buffer[seqi], xa_d1s[tid], xa_i_1);
seqio[seqi].xa_d1s = xa_d1s_buffer[seqi];
memcpy(sam_pos1s_buffer[seqi], sam_pos1s[tid], xa_i_1 << 2);
seqio[seqi].sam_pos1s = sam_pos1s_buffer[seqi];
memcpy(lv_re1s_buffer[seqi], lv_re1s[tid], xa_i_1 << 2);
seqio[seqi].lv_re1s = lv_re1s_buffer[seqi];
for(v_cnt_i = 0; v_cnt_i < xa_i_1; v_cnt_i++)
{
pos_l = strlen(cigar_p1s[tid][v_cnt_i]) + 1;
seqio[seqi].cigar_p1s[v_cnt_i] = (char* )malloc(pos_l);
memcpy(seqio[seqi].cigar_p1s[v_cnt_i], cigar_p1s[tid][v_cnt_i], pos_l);
}
}
if(xa_i_2 > 0)
{
//memcpy(chr_res_buffer[seqi], chr_res[tid], xa_i_2 << 2);
//seqio[seqi].chr_res = chr_res_buffer[seqi];
memcpy(xa_d2s_buffer[seqi], xa_d2s[tid], xa_i_2);
seqio[seqi].xa_d2s = xa_d2s_buffer[seqi];
memcpy(sam_pos2s_buffer[seqi], sam_pos2s[tid], xa_i_2 << 2);
seqio[seqi].sam_pos2s = sam_pos2s_buffer[seqi];
memcpy(lv_re2s_buffer[seqi], lv_re2s[tid], xa_i_2 << 2);
seqio[seqi].lv_re2s = lv_re2s_buffer[seqi];
for(v_cnt_i = 0; v_cnt_i < xa_i_2; v_cnt_i++)
{
pos_l = strlen(cigar_p2s[tid][v_cnt_i]) + 1;
seqio[seqi].cigar_p2s[v_cnt_i] = (char* )malloc(pos_l);
memcpy(seqio[seqi].cigar_p2s[v_cnt_i], cigar_p2s[tid][v_cnt_i], pos_l);
}
}
#endif
}
else
{
//seqio[seqi].xa_n = 0;
seqio[seqi].xa_n_p1 = 0;
seqio[seqi].xa_n_p2 = 0;
#ifdef FIX_SV
seqio[seqi].xa_n_x1 = 0;
seqio[seqi].xa_n_x2 = 0;
#endif
seqio[seqi].xa_n1 = 0;
seqio[seqi].xa_n2 = 0;
seqio[seqi].flag1 = 77;
seqio[seqi].flag2 = 141;
//seqio[seqi].chr_re = chr_file_n;
seqio[seqi].chr_re1 = chr_file_n;
seqio[seqi].chr_re2 = chr_file_n;
seqio[seqi].pos1 = 0;
seqio[seqi].pos2 = 0;
seqio[seqi].qualc1 = 0;
seqio[seqi].qualc2 = 0;
strcpy(pr_cigar1_buffer[seqi], "*");
seqio[seqi].cigar1 = pr_cigar1_buffer[seqi];
strcpy(pr_cigar2_buffer[seqi], "*");
seqio[seqi].cigar2 = pr_cigar2_buffer[seqi];
seqio[seqi].seq1 = seqio[seqi].read_seq1;
seqio[seqi].seq2 = seqio[seqi].read_seq2;
}
}
#else
seqio[seqi].v_cnt = 0;
#endif
}
return 0;
}
#ifdef UNPIPATH_OFF_K20
seed_pa_single* single_seed_reduction_core_single64(seed_pa_single* seedpa, uint64_t* read_bit, uint8_t* read_val, uint64_t** seed_set_pos, uint8_t tid, uint16_t read_length, uint16_t* max_seed_length, uint8_t rc_i)
#else
seed_pa_single* single_seed_reduction_core_single(seed_pa_single* seedpa, uint64_t* read_bit, uint8_t* read_val, uint32_t** seed_set_pos, uint8_t tid, uint16_t read_length, uint16_t* max_seed_length, uint8_t rc_i)
#endif
{
#ifdef UNPIPATH_OFF_K20
uint64_t kmer_pos_uni = 0;
uint64_t* pos_tmp_p = NULL;
#else
uint32_t kmer_pos_uni = 0;
uint32_t* pos_tmp_p = NULL;
#endif
uint8_t pop_i = 0;
uint8_t re_d = 0;
uint8_t b_t_n_r = 0;
uint16_t left_i = 1;
uint16_t right_i = 1;
uint16_t read_off = 0;
uint16_t read_pos = 0;
uint16_t length = 0;
uint16_t rt_pos = 0;
uint16_t mem_i = 0;
uint16_t r_b_v = 0;
uint16_t su_i = 0;
uint16_t seed_set_i = 0;
uint16_t cov_i = 0;
uint32_t seed_i = 0;
uint32_t uni_offset_s_l = 0;
uint32_t uni_offset_s_r = 0;
uint32_t ref_pos_n = 0;
uint32_t uni_id = 0;
uint32_t seed_hash = 0;
uint32_t seed_kmer = 0;
uint32_t uni_id_tmp = 0Xffffffff;
uint32_t spa_i = 0;
uint32_t pos_n = 0;
uint32_t set_n = 0;
uint32_t b_p_i = 0;
uint32_t id_i = 0;
uint32_t off_n = 0;
uint32_t off_i = 0;
uint32_t set_pos_n = 0;
uint32_t pos_start_off = 0;
uint32_t set_i = 0;
uint32_t set_i_pre = 0;
uint32_t seed_same_n = 0;
uint32_t max_sets_n = 0;
uint32_t interval_n = 0;
uint32_t bn = 0;
uint32_t sn = 0;
int r_p1 = 0;
int set_c_r = 0;
uint64_t kmer_bit = 0;
int64_t posp = 0;
int64_t reduce_pn = 0;
int64_t reduce_p = 0;
int64_t reduce_sn = 0;
int64_t reduce_s = 0;
int64_t b_r_s = 0;
int64_t seed_binary_r = 0;
int64_t seed_id_r = 0;
int64_t ref_off1 = 0;
seed_m* seed_tmp = NULL;
#ifdef SINGLE_PAIR
uint16_t cov_num_front = 0;
uint16_t cov_num_re = 0;
uint16_t length_front = 0;
uint16_t length_back = 0;
#endif
mem_i = 0;
r_b_v = 0;
for(read_off = 0; read_off <= read_length - k_t; read_off += seed_l[tid])
{
if(read_off + k_t - 1 <= r_b_v) continue;
re_d = (read_off & 0X1f);
b_t_n_r = 32 - re_d;
#ifdef HASH_KMER_READ_J
if(re_d <= re_b)
{
kmer_bit = ((read_bit[read_off >> 5] & bit_tran_re[re_d]) >> ((re_b - re_d) << 1));
}
else
{
kmer_bit = (((read_bit[read_off >> 5] & bit_tran_re[re_d]) << ((re_d - re_b) << 1)) | (read_bit[(read_off >> 5) + 1] >> ((re_2bt - re_d) << 1)));
}
#else
tran_tmp_p = (read_bit[read_off >> 5] & bit_tran_re[re_d]);
//or use this method to deal with: & bit_tran_re[b_t_n_r]
kmer_bit = (((read_bit[(read_off >> 5) + 1] >> (b_t_n_r << 1)) & bit_tran_re[b_t_n_r]) | (tran_tmp_p << (re_d << 1)));
kmer_bit >>= re_bt;
#endif
seed_kmer = (kmer_bit & bit_tran[k_r]);
seed_hash = (kmer_bit >> (k_r << 1));
//find the kmer
#ifdef UNPIPATH_OFF_K20
seed_binary_r = binsearch_offset64(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#else
seed_binary_r = binsearch_offset(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#endif
if(seed_binary_r == -1)
continue;
//binary search on unipath offset to get the unipathID
kmer_pos_uni = buffer_off_g[seed_binary_r];//this kmer's offset on unipath
#ifdef UNPIPATH_OFF_K20
seed_id_r = binsearch_interval_unipath64(kmer_pos_uni, buffer_seqf, result_seqf);
#else
seed_id_r = binsearch_interval_unipath(kmer_pos_uni, buffer_seqf, result_seqf);
#endif
ref_pos_n = buffer_pp[seed_id_r + 1] - buffer_pp[seed_id_r];
if(ref_pos_n > pos_n_max)
{
continue;
}
uni_offset_s_l = kmer_pos_uni - buffer_seqf[seed_id_r];
uni_offset_s_r = buffer_seqf[seed_id_r + 1] - (kmer_pos_uni + k_t);
for(left_i = 1; (left_i <= uni_offset_s_l) && (left_i <= read_off); left_i++)
{
#ifdef UNI_SEQ64
if(((buffer_seq[(kmer_pos_uni - left_i) >> 5] >> ((31 - ((kmer_pos_uni - left_i) & 0X1f)) << 1)) & 0X3)
!= ((read_bit[(read_off - left_i) >> 5] >> ((31 - ((read_off - left_i) & 0X1f)) << 1)) & 0X3)
) break;
#else
if(((buffer_seq[(kmer_pos_uni - left_i) >> 2] >> (((kmer_pos_uni - left_i) & 0X3) << 1)) & 0X3)
!= ((read_bit[(read_off - left_i) >> 5] >> ((31 - ((read_off - left_i) & 0X1f)) << 1)) & 0X3)
) break;
#endif
}
for(right_i = 1; (right_i <= uni_offset_s_r) && (right_i <= read_length - read_off - k_t); right_i++)
{
#ifdef UNI_SEQ64
if(((buffer_seq[(kmer_pos_uni + k_t - 1 + right_i) >> 5] >> ((31 - ((kmer_pos_uni + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
!= ((read_bit[(read_off + k_t - 1 + right_i) >> 5] >> ((31 - ((read_off + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
) break;
#else
if(((buffer_seq[(kmer_pos_uni + k_t - 1 + right_i) >> 2] >> (((kmer_pos_uni + k_t - 1 + right_i) & 0X3) << 1)) & 0X3)
!= ((read_bit[(read_off + k_t - 1 + right_i) >> 5] >> ((31 - ((read_off + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
) break;
#endif
}
read_pos = read_off + 1 - left_i;
length = k_t + left_i + right_i - 2;
rt_pos = read_off + k_t + right_i - 2;
seedm[tid][mem_i].uni_id = seed_id_r;
seedm[tid][mem_i].length = length;
seedm[tid][mem_i].read_pos = read_pos;
seedm[tid][mem_i].ref_pos_off = uni_offset_s_l + 1 - left_i;
seedm[tid][mem_i].ref_pos_n = ref_pos_n;
if((left_i - 1 < read_off) || (right_i - 1 < read_length - read_off - k_t))
{
seedm[tid][mem_i].ui = 0;
}
else
{
seedm[tid][mem_i].ui = 1;
seedm[tid][mem_i].ref_pos_off_r = uni_offset_s_r + 1 - right_i;
}
seedm[tid][mem_i].s_r_o_l = read_off - left_i;
seedm[tid][mem_i].s_r_o_r = read_off + k_t + right_i - 1;
memset(seedm[tid][mem_i].cov, 0Xff, (cov_a_n_s[tid]) << 3);
(seedm[tid][mem_i].cov)[read_pos >> 6] = bv_64[(64 - (read_pos & 0X3f))];
(seedm[tid][mem_i].cov)[rt_pos >> 6] ^= bv_64[(63 - (rt_pos & 0X3f))];
for(cov_i = (read_pos >> 6); cov_i > 0; cov_i--)
(seedm[tid][mem_i].cov)[cov_i - 1] = 0;
for(cov_i = (rt_pos >> 6) + 1; cov_i < cov_a_n_s[tid]; cov_i++)
(seedm[tid][mem_i].cov)[cov_i] = 0;
seedm[tid][mem_i].tid = tid;
r_b_v = read_off + k_t + right_i - 1;
++mem_i;
}
//end MEM
if(mem_i == 0) return 0;
//merge seeds in the same unipath
s_uid_f[tid] = 0;
qsort(seedm[tid], mem_i, sizeof(seed_m), compare_uniid);
if(s_uid_f[tid] == 1)
{
su_i = 0;
for(seed_i = 0; seed_i < mem_i; seed_i++)
{
if(uni_id_tmp != seedm[tid][seed_i].uni_id)
{
seedu[tid][su_i].uni_id = seedm[tid][seed_i].uni_id;
seedu[tid][su_i].read_pos = seedm[tid][seed_i].read_pos;
seedu[tid][su_i].ref_pos_off = seedm[tid][seed_i].ref_pos_off;
seedu[tid][su_i].ref_pos_off_r = seedm[tid][seed_i].ref_pos_off_r;
seedu[tid][su_i].ui = seedm[tid][seed_i].ui;
seedu[tid][su_i].s_r_o_l = seedm[tid][seed_i].s_r_o_l;
seedu[tid][su_i].s_r_o_r = seedm[tid][seed_i].s_r_o_r;
seedu[tid][su_i].ref_pos_n = seedm[tid][seed_i].ref_pos_n;
memcpy(seedu[tid][su_i].cov, seedm[tid][seed_i].cov, (cov_a_n_s[tid]) << 3);
seedu[tid][su_i].tid = tid;
//cal length
if(su_i > 0)
{
seedu[tid][su_i - 1].length = 0;
for(cov_i = 0; cov_i < cov_a_n_s[tid]; cov_i++)
seedu[tid][su_i - 1].length += popcount_3((seedu[tid][su_i - 1].cov)[cov_i]);
}
++su_i;
}
else
{
for(cov_i = 0; cov_i < cov_a_n_s[tid]; cov_i++)
(seedu[tid][su_i - 1].cov)[cov_i] |= (seedm[tid][seed_i].cov)[cov_i];
}
uni_id_tmp = seedm[tid][seed_i].uni_id;
}
seedu[tid][su_i - 1].length = 0;
for(cov_i = 0; cov_i < cov_a_n_s[tid]; cov_i++)
seedu[tid][su_i - 1].length += popcount_3((seedu[tid][su_i - 1].cov)[cov_i]);
//end merge of same unipath
seed_tmp = seedu[tid];
}
else
{
su_i = mem_i;
seed_tmp = seedm[tid];
}
//add print
for ( seed_i = 0; seed_i < su_i; ++seed_i)
{
fprintf(stderr, "read_pos = %u, length = %u\n", seedu[tid][seed_i].read_pos, seedu[tid][seed_i].length);
}
//uniqueness
qsort(seed_tmp, su_i, sizeof(seed_m), compare_posn);
uni_id = seed_tmp[0].uni_id;
ref_off1 = seed_tmp[0].ref_pos_off;
r_p1 = seed_tmp[0].read_pos;
pos_tmp_p = buffer_p + buffer_pp[uni_id];
pos_n = buffer_pp[uni_id + 1] - buffer_pp[uni_id];
//fingerprint
for(id_i = 0; id_i < pos_n; id_i++)
{
seedsets[tid][id_i].seed_set = pos_tmp_p[id_i] + ref_off1 - r_p1;
memcpy(seedsets[tid][id_i].cov, seed_tmp[0].cov, (cov_a_n_s[tid]) << 3);
seedsets[tid][id_i].ui = seed_tmp[0].ui;
seedsets[tid][id_i].ref_pos_off = ref_off1;
seedsets[tid][id_i].ref_pos_off_r = seed_tmp[0].ref_pos_off_r;
seedsets[tid][id_i].s_r_o_l = seed_tmp[0].s_r_o_l;
seedsets[tid][id_i].s_r_o_r = seed_tmp[0].s_r_o_r;
seedsets[tid][id_i].tid = tid;
}
set_n += pos_n;
seed_set_off[tid][0] = 0;
seed_set_off[tid][1] = pos_n;
off_n += 2;
#ifdef MERGE_B_R_VS
for(seed_i = 1; seed_i < su_i; seed_i++)
{
uni_id = seed_tmp[seed_i].uni_id;
ref_off1 = seed_tmp[seed_i].ref_pos_off;
r_p1 = seed_tmp[seed_i].read_pos;
reduce_pn = buffer_pp[uni_id + 1];
bn = reduce_pn - buffer_pp[uni_id];
for(seed_set_i = 0; seed_set_i < seed_i; seed_set_i++)
{
reduce_sn = seed_set_off[tid][seed_set_i + 1];
sn = reduce_sn - seed_set_off[tid][seed_set_i];
if(bn <= sn)
{
reduce_s = seed_set_off[tid][seed_set_i];
for(b_p_i = buffer_pp[uni_id]; b_p_i < reduce_pn; b_p_i++)
{
posp = buffer_p[b_p_i] + ref_off1 - r_p1;
#ifdef UNPIPATH_OFF_K20
b_r_s = binsearch_seed_set_reduce64(posp, seedsets[tid], reduce_sn - reduce_s, reduce_s, tid);
#else
b_r_s = binsearch_seed_set_reduce(posp, seedsets[tid], reduce_sn - reduce_s, reduce_s, tid);
#endif
if(b_r_s != -1)
{
for(cov_i = 0; cov_i < cov_a_n_s[tid]; cov_i++)
(seedsets[tid][b_r_s].cov)[cov_i] |= (seed_tmp[seed_i].cov)[cov_i];
pos_add[tid][b_p_i - buffer_pp[uni_id]] = 1;
if(b_r_s == reduce_sn - 1)
break;
reduce_s = b_r_s + 1;
}
else
{
if(g_low[tid] == reduce_sn - reduce_s)
break;
else reduce_s += g_low[tid];
}
}
}
else
{
reduce_p = buffer_pp[uni_id];
for(b_p_i = seed_set_off[tid][seed_set_i]; b_p_i < reduce_sn; b_p_i++)
{
posp = seedsets[tid][b_p_i].seed_set + r_p1 - ref_off1;
#ifdef UNPIPATH_OFF_K20
b_r_s = binsearch_seed_pos_reduce64(posp, buffer_p, reduce_pn - reduce_p, reduce_p, tid);
#else
b_r_s = binsearch_seed_pos_reduce(posp, buffer_p, reduce_pn - reduce_p, reduce_p, tid);
#endif
if(b_r_s != -1)
{
for(cov_i = 0; cov_i < cov_a_n_s[tid]; cov_i++)
(seedsets[tid][b_p_i].cov)[cov_i] |= (seed_tmp[seed_i].cov)[cov_i];
pos_add[tid][b_r_s - buffer_pp[uni_id]] = 1;
if(b_r_s == reduce_pn - 1)
break;
reduce_p = b_r_s + 1;
}
else
{
if(g_low[tid] == reduce_pn - reduce_p)
break;
else reduce_p += g_low[tid];
}
}
}
}
for(b_p_i = 0; b_p_i < bn; b_p_i++)
{
if(pos_add[tid][b_p_i] == 0)
{
seedsets[tid][set_n].seed_set = buffer_p[buffer_pp[uni_id] + b_p_i] + ref_off1 - r_p1;
memcpy(seedsets[tid][set_n].cov, seed_tmp[seed_i].cov, (cov_a_n_s[tid]) << 3);
seedsets[tid][set_n].ui = seed_tmp[seed_i].ui;
seedsets[tid][set_n].ref_pos_off = ref_off1;
seedsets[tid][set_n].ref_pos_off_r = seed_tmp[seed_i].ref_pos_off_r;
seedsets[tid][set_n].s_r_o_l = seed_tmp[seed_i].s_r_o_l;
seedsets[tid][set_n].s_r_o_r = seed_tmp[seed_i].s_r_o_r;
seedsets[tid][set_n].tid = tid;
++set_n;
}
}
memset(pos_add[tid], 0, bn);
seed_set_off[tid][seed_i + 1] = set_n;
++off_n;
}
#endif
#ifdef SINGLE_PAIR
cov_num_front = cov_num_front_single[tid];
cov_num_re = cov_num_re_single[tid];
#endif
spa_i = spa_i_single[tid];
set_pos_n = set_pos_n_single[tid];
pos_start_off = set_pos_n_single[tid];
for(off_i = 0; off_i < off_n - 1; off_i++)
{
interval_n = seed_set_off[tid][off_i + 1] - seed_set_off[tid][off_i];
if(interval_n == 0) continue;
qsort(seedsets[tid] + seed_set_off[tid][off_i], interval_n, sizeof(seed_sets), compare_sets_s);
//copy elements from seed_tmp[off_i] as for other elements such as quality
set_i_pre = seed_set_off[tid][off_i];
seedpa[spa_i].rc = rc_i;
seedpa[spa_i].pos_start = set_i_pre + pos_start_off;
memcpy(seedpa[spa_i].cov, seedsets[tid][set_i_pre].cov, (cov_a_n_s[tid]) << 3);
seedpa[spa_i].ref_pos_off = seedsets[tid][set_i_pre].ref_pos_off;
seedpa[spa_i].ref_pos_off_r = seedsets[tid][set_i_pre].ref_pos_off_r;
seedpa[spa_i].ui = seedsets[tid][set_i_pre].ui;
seedpa[spa_i].s_r_o_l = seedsets[tid][set_i_pre].s_r_o_l;
seedpa[spa_i].s_r_o_r = seedsets[tid][set_i_pre].s_r_o_r;
#ifdef SINGLE_PAIR
length_front = 0;
length_back = 0;
for(pop_i = 0; pop_i < cov_num_front; pop_i++)
length_front += popcount_3((seedpa[spa_i].cov)[pop_i]);
length_front += popcount_3(((seedpa[spa_i].cov)[cov_num_front]) >> cov_num_re);
length_back += popcount_3(((seedpa[spa_i].cov)[cov_num_front]) & bv_64[cov_num_re]);
for(pop_i = cov_num_front + 1; pop_i < cov_a_n_s[tid]; pop_i++)
length_back += popcount_3((seedpa[spa_i].cov)[pop_i]);
seedpa[spa_i].length = length_front + length_back;
if(seedpa[spa_i].length > max_sets_n) max_sets_n = seedpa[spa_i].length;
if((length_front > k_t) && (length_back > k_t)) seedpa[spa_i].pair_flag = 1;
else seedpa[spa_i].pair_flag = 0;
#else
//cal number of 1 (length)
seedpa[spa_i].length = 0;
for(pop_i = 0; pop_i < cov_a_n_s[tid]; pop_i++)
seedpa[spa_i].length += popcount_3((seedpa[spa_i].cov)[pop_i]);
if(seedpa[spa_i].length > max_sets_n) max_sets_n = seedpa[spa_i].length;
#endif
++spa_i;
seed_same_n = 1;
//copy pos to seed_set_pos
(*seed_set_pos)[set_pos_n++] = seedsets[tid][set_i_pre].seed_set; //+ ref_off - r_p
for(set_i = set_i_pre + 1; set_i < seed_set_off[tid][off_i + 1]; set_i++)
{
set_c_r = memcmp(seedsets[tid][set_i_pre].cov, seedsets[tid][set_i].cov, (cov_a_n_s[tid]) << 3);
if(set_c_r != 0)
{
seedpa[spa_i - 1].pos_n = seed_same_n;
//copy elements from seed_tmp[off_i] as for other elements such as quality
seedpa[spa_i].rc = rc_i;
seedpa[spa_i].pos_start = set_i + pos_start_off;
memcpy(seedpa[spa_i].cov, seedsets[tid][set_i].cov, (cov_a_n_s[tid]) << 3);
seedpa[spa_i].ref_pos_off = seedsets[tid][set_i].ref_pos_off;
seedpa[spa_i].ref_pos_off_r = seedsets[tid][set_i].ref_pos_off_r;
seedpa[spa_i].ui = seedsets[tid][set_i].ui;
seedpa[spa_i].s_r_o_l = seedsets[tid][set_i].s_r_o_l;
seedpa[spa_i].s_r_o_r = seedsets[tid][set_i].s_r_o_r;
#ifdef SINGLE_PAIR
length_front = 0;
length_back = 0;
for(pop_i = 0; pop_i < cov_num_front; pop_i++)
length_front += popcount_3((seedpa[spa_i].cov)[pop_i]);
length_front += popcount_3(((seedpa[spa_i].cov)[cov_num_front]) >> cov_num_re);
length_back += popcount_3(((seedpa[spa_i].cov)[cov_num_front]) & bv_64[cov_num_re]);
for(pop_i = cov_num_front + 1; pop_i < cov_a_n_s[tid]; pop_i++)
length_back += popcount_3((seedpa[spa_i].cov)[pop_i]);
seedpa[spa_i].length = length_front + length_back;
if(seedpa[spa_i].length > max_sets_n) max_sets_n = seedpa[spa_i].length;
if((length_front > k_t) && (length_back > k_t)) seedpa[spa_i].pair_flag = 1;
else seedpa[spa_i].pair_flag = 0;
#else
//cal number of 1 (length)
seedpa[spa_i].length = 0;
for(pop_i = 0; pop_i < cov_a_n_s[tid]; pop_i++)
seedpa[spa_i].length += popcount_3((seedpa[spa_i].cov)[pop_i]);
if(seedpa[spa_i].length > max_sets_n) max_sets_n = seedpa[spa_i].length;
#endif
++spa_i;
seed_same_n = 1;
}
else ++seed_same_n;
//copy pos to seed_set_pos
(*seed_set_pos)[set_pos_n++] = seedsets[tid][set_i].seed_set;// + ref_off - r_p
set_i_pre = set_i;
}
seedpa[spa_i - 1].pos_n = seed_same_n;
}
set_pos_n_single[tid] = set_pos_n;
//qsort(seedpa, spa_i, sizeof(seed_pa), compare_plen);
spa_i_single[tid] = spa_i;
(*max_seed_length) = max_sets_n;
return seedpa;
}
#ifdef UNPIPATH_OFF_K20
seed_pa* single_seed_reduction_core_filter64(seed_pa* seedpa, uint64_t* read_bit, uint8_t* read_val, uint32_t* spa1_i, uint64_t** seed_set_pos, uint16_t* pos_ren, uint8_t tid, uint16_t read_length, uint16_t* seed_num, uint16_t* max_seed_length)
#else
seed_pa* single_seed_reduction_core_filter(seed_pa* seedpa, uint64_t* read_bit, uint8_t* read_val, uint32_t* spa1_i, uint32_t** seed_set_pos, uint16_t* pos_ren, uint8_t tid, uint16_t read_length, uint16_t* seed_num, uint16_t* max_seed_length)
#endif
{
uint8_t pop_i = 0;
uint8_t re_d = 0;
uint8_t b_t_n_r = 0;
uint8_t cov_a_t = 0;
uint16_t left_i = 1;
uint16_t right_i = 1;
uint16_t read_off = 0;
uint16_t read_pos = 0;
uint16_t length = 0;
uint16_t rt_pos = 0;
uint16_t mem_i = 0;
uint16_t r_b_v = 0;
uint16_t su_i = 0;
uint16_t seed_set_i = 0;
uint16_t cov_i = 0;
uint32_t seed_i = 0;
uint32_t uni_offset_s_l = 0;
uint32_t uni_offset_s_r = 0;
uint32_t ref_pos_n = 0;
uint32_t seed_hash = 0;
uint32_t seed_kmer = 0;
uint32_t uni_id_tmp = 0Xffffffff;
uint32_t spa_i = 0;
uint32_t pos_n = 0;
uint32_t set_n = 0;
uint32_t id_i = 0;
uint32_t off_n = 0;
uint32_t off_i = 0;
uint32_t set_pos_n = 0;
uint32_t set_i = 0;
uint32_t set_i_pre = 0;
uint32_t seed_same_n = 0;
uint32_t max_sets_n = 0;
uint32_t interval_n = 0;
uint32_t bn = 0;
uint32_t sn = 0;
#ifdef UNPIPATH_OFF_K20
uint64_t* pos_tmp_p = NULL;
uint64_t kmer_pos_uni = 0;
uint64_t b_p_i = 0;
uint64_t uni_id = 0;
#else
uint32_t* pos_tmp_p = NULL;
uint32_t kmer_pos_uni = 0;
uint32_t b_p_i = 0;
uint32_t uni_id = 0;
#endif
int r_p1 = 0;
int set_c_r = 0;
uint64_t kmer_bit = 0;
int64_t posp = 0;
int64_t reduce_pn = 0;
int64_t reduce_p = 0;
int64_t reduce_sn = 0;
int64_t reduce_s = 0;
int64_t b_r_s = 0;
int64_t seed_binary_r = 0;
int64_t seed_id_r = 0;
int64_t ref_off1 = 0;
cov_a_t = cov_a_n[tid][rc_cov_f[tid]];
seed_m* seed_tmp = NULL;
mem_i = 0;
r_b_v = 0;
for(read_off = 0; read_off <= read_length - k_t; read_off += seed_l[tid])
{
if(read_off + k_t - 1 <= r_b_v) continue;
re_d = (read_off & 0X1f);
b_t_n_r = 32 - re_d;
#ifdef HASH_KMER_READ_J
if(re_d <= re_b)
{
kmer_bit = ((read_bit[read_off >> 5] & bit_tran_re[re_d]) >> ((re_b - re_d) << 1));
}
else
{
kmer_bit = (((read_bit[read_off >> 5] & bit_tran_re[re_d]) << ((re_d - re_b) << 1)) | (read_bit[(read_off >> 5) + 1] >> ((re_2bt - re_d) << 1)));
}
#else
tran_tmp_p = (read_bit[read_off >> 5] & bit_tran_re[re_d]);
//or use this method to deal with: & bit_tran_re[b_t_n_r]
kmer_bit = (((read_bit[(read_off >> 5) + 1] >> (b_t_n_r << 1)) & bit_tran_re[b_t_n_r]) | (tran_tmp_p << (re_d << 1)));
kmer_bit >>= re_bt;
#endif
seed_kmer = (kmer_bit & bit_tran[k_r]);
seed_hash = (kmer_bit >> (k_r << 1));
//find the kmer
#ifdef UNPIPATH_OFF_K20
seed_binary_r = binsearch_offset64(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#else
seed_binary_r = binsearch_offset(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#endif
if(seed_binary_r == -1)
continue;
//binary search on unipath offset to get the unipathID
kmer_pos_uni = buffer_off_g[seed_binary_r];//this kmer's offset on unipath
#ifdef UNPIPATH_OFF_K20
seed_id_r = binsearch_interval_unipath64(kmer_pos_uni, buffer_seqf, result_seqf);
#else
seed_id_r = binsearch_interval_unipath(kmer_pos_uni, buffer_seqf, result_seqf);
#endif
ref_pos_n = buffer_pp[seed_id_r + 1] - buffer_pp[seed_id_r];
if(ref_pos_n > pos_n_max)
{
#ifdef PAIR_RANDOM
if(seed_l[tid] == pair_ran_intvp) (*pos_ren)++;
#endif
continue;
}
uni_offset_s_l = kmer_pos_uni - buffer_seqf[seed_id_r];
uni_offset_s_r = buffer_seqf[seed_id_r + 1] - (kmer_pos_uni + k_t);
for(left_i = 1; (left_i <= uni_offset_s_l) && (left_i <= read_off); left_i++)
{
#ifdef UNI_SEQ64
if(((buffer_seq[(kmer_pos_uni - left_i) >> 5] >> ((31 - ((kmer_pos_uni - left_i) & 0X1f)) << 1)) & 0X3)
!= ((read_bit[(read_off - left_i) >> 5] >> ((31 - ((read_off - left_i) & 0X1f)) << 1)) & 0X3)
) break;
#else
if(((buffer_seq[(kmer_pos_uni - left_i) >> 2] >> (((kmer_pos_uni - left_i) & 0X3) << 1)) & 0X3)
!= ((read_bit[(read_off - left_i) >> 5] >> ((31 - ((read_off - left_i) & 0X1f)) << 1)) & 0X3)
) break;
#endif
}
for(right_i = 1; (right_i <= uni_offset_s_r) && (right_i <= read_length - read_off - k_t); right_i++)
{
#ifdef UNI_SEQ64
if(((buffer_seq[(kmer_pos_uni + k_t - 1 + right_i) >> 5] >> ((31 - ((kmer_pos_uni + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
!= ((read_bit[(read_off + k_t - 1 + right_i) >> 5] >> ((31 - ((read_off + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
) break;
#else
if(((buffer_seq[(kmer_pos_uni + k_t - 1 + right_i) >> 2] >> (((kmer_pos_uni + k_t - 1 + right_i) & 0X3) << 1)) & 0X3)
!= ((read_bit[(read_off + k_t - 1 + right_i) >> 5] >> ((31 - ((read_off + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
) break;
#endif
}
read_pos = read_off + 1 - left_i;
length = k_t + left_i + right_i - 2;
rt_pos = read_off + k_t + right_i - 2;
seedm[tid][mem_i].uni_id = seed_id_r;
seedm[tid][mem_i].length = length;
seedm[tid][mem_i].read_pos = read_pos;
seedm[tid][mem_i].ref_pos_off = uni_offset_s_l + 1 - left_i;
seedm[tid][mem_i].ref_pos_n = ref_pos_n;
if((left_i - 1 < read_off) || (right_i - 1 < read_length - read_off - k_t)) //cross the unipath
{
seedm[tid][mem_i].ui = 0;
}
else
{
seedm[tid][mem_i].ui = 1;
seedm[tid][mem_i].ref_pos_off_r = uni_offset_s_r + 1 - right_i;
}
seedm[tid][mem_i].s_r_o_l = read_off - left_i;
seedm[tid][mem_i].s_r_o_r = read_off + k_t + right_i - 1;
memset(seedm[tid][mem_i].cov, 0Xff, (cov_a_t) << 3);
(seedm[tid][mem_i].cov)[read_pos >> 6] = bv_64[(64 - (read_pos & 0X3f))];
(seedm[tid][mem_i].cov)[rt_pos >> 6] ^= bv_64[(63 - (rt_pos & 0X3f))];
for(cov_i = (read_pos >> 6); cov_i > 0; cov_i--)
(seedm[tid][mem_i].cov)[cov_i - 1] = 0;
for(cov_i = (rt_pos >> 6) + 1; cov_i < cov_a_t; cov_i++)
(seedm[tid][mem_i].cov)[cov_i] = 0;
seedm[tid][mem_i].tid = tid;
r_b_v = read_off + k_t + right_i - 1;
++mem_i;
}
//end MEM
if(mem_i == 0) return 0;
//merge seeds in the same unipath
s_uid_f[tid] = 0;
qsort(seedm[tid], mem_i, sizeof(seed_m), compare_uniid);
if(s_uid_f[tid] == 1)
{
su_i = 0;
for(seed_i = 0; seed_i < mem_i; seed_i++)
{
if(uni_id_tmp != seedm[tid][seed_i].uni_id)
{
seedu[tid][su_i].uni_id = seedm[tid][seed_i].uni_id;
seedu[tid][su_i].read_pos = seedm[tid][seed_i].read_pos;//choose the one with more ref positions
seedu[tid][su_i].ref_pos_off = seedm[tid][seed_i].ref_pos_off;
seedu[tid][su_i].ref_pos_off_r = seedm[tid][seed_i].ref_pos_off_r;
seedu[tid][su_i].ui = seedm[tid][seed_i].ui;
seedu[tid][su_i].s_r_o_l = seedm[tid][seed_i].s_r_o_l;
seedu[tid][su_i].s_r_o_r = seedm[tid][seed_i].s_r_o_r;
seedu[tid][su_i].ref_pos_n = seedm[tid][seed_i].ref_pos_n;
memcpy(seedu[tid][su_i].cov, seedm[tid][seed_i].cov, (cov_a_t) << 3);
seedu[tid][su_i].tid = tid;
//cal length
if(su_i > 0)
{
seedu[tid][su_i - 1].length = 0;
for(cov_i = 0; cov_i < cov_a_t; cov_i++)
seedu[tid][su_i - 1].length += popcount_3((seedu[tid][su_i - 1].cov)[cov_i]);
}
++su_i;
}
else
{
for(cov_i = 0; cov_i < cov_a_t; cov_i++)
(seedu[tid][su_i - 1].cov)[cov_i] |= (seedm[tid][seed_i].cov)[cov_i];
}
uni_id_tmp = seedm[tid][seed_i].uni_id;
}
seedu[tid][su_i - 1].length = 0;
for(cov_i = 0; cov_i < cov_a_t; cov_i++)
seedu[tid][su_i - 1].length += popcount_3((seedu[tid][su_i - 1].cov)[cov_i]);
//end merge of same unipath
seed_tmp = seedu[tid];
}
else
{
su_i = mem_i;
seed_tmp = seedm[tid];
}
//uniqueness
qsort(seed_tmp, su_i, sizeof(seed_m), compare_posn);
uni_id = seed_tmp[0].uni_id;
ref_off1 = seed_tmp[0].ref_pos_off;
r_p1 = seed_tmp[0].read_pos;
pos_tmp_p = buffer_p + buffer_pp[uni_id];//119843814
pos_n = buffer_pp[uni_id + 1] - buffer_pp[uni_id];
//fingerprint
for(id_i = 0; id_i < pos_n; id_i++)
{
seedsets[tid][id_i].seed_set = pos_tmp_p[id_i] + ref_off1 - r_p1;
memcpy(seedsets[tid][id_i].cov, seed_tmp[0].cov, (cov_a_t) << 3);
seedsets[tid][id_i].ui = seed_tmp[0].ui;
seedsets[tid][id_i].ref_pos_off = ref_off1;
seedsets[tid][id_i].ref_pos_off_r = seed_tmp[0].ref_pos_off_r;
seedsets[tid][id_i].s_r_o_l = seed_tmp[0].s_r_o_l;
seedsets[tid][id_i].s_r_o_r = seed_tmp[0].s_r_o_r;
seedsets[tid][id_i].tid = tid;
}
set_n += pos_n;
seed_set_off[tid][0] = 0;
seed_set_off[tid][1] = pos_n;
off_n += 2;
#ifdef MERGE_B_R_VS
for(seed_i = 1; seed_i < su_i; seed_i++)
{
uni_id = seed_tmp[seed_i].uni_id;
ref_off1 = seed_tmp[seed_i].ref_pos_off;
r_p1 = seed_tmp[seed_i].read_pos;
reduce_pn = buffer_pp[uni_id + 1];
bn = reduce_pn - buffer_pp[uni_id];
for(seed_set_i = 0; seed_set_i < seed_i; seed_set_i++)
{
reduce_sn = seed_set_off[tid][seed_set_i + 1];
sn = reduce_sn - seed_set_off[tid][seed_set_i];
if(bn <= sn)
{
reduce_s = seed_set_off[tid][seed_set_i];
for(b_p_i = buffer_pp[uni_id]; b_p_i < reduce_pn; b_p_i++)
{
posp = buffer_p[b_p_i] + ref_off1 - r_p1;
#ifdef UNPIPATH_OFF_K20
b_r_s = binsearch_seed_set_reduce64(posp, seedsets[tid], reduce_sn - reduce_s, reduce_s, tid);
#else
b_r_s = binsearch_seed_set_reduce(posp, seedsets[tid], reduce_sn - reduce_s, reduce_s, tid);
#endif
if(b_r_s != -1)
{
for(cov_i = 0; cov_i < cov_a_t; cov_i++)
(seedsets[tid][b_r_s].cov)[cov_i] |= (seed_tmp[seed_i].cov)[cov_i];
pos_add[tid][b_p_i - buffer_pp[uni_id]] = 1;
if(b_r_s == reduce_sn - 1)
break;
reduce_s = b_r_s + 1;
}
else
{
if(g_low[tid] == reduce_sn - reduce_s)
break;
else reduce_s += g_low[tid];
}
}
}
else
{
reduce_p = buffer_pp[uni_id];
for(b_p_i = seed_set_off[tid][seed_set_i]; b_p_i < reduce_sn; b_p_i++)
{
posp = seedsets[tid][b_p_i].seed_set + r_p1 - ref_off1;
#ifdef UNPIPATH_OFF_K20
b_r_s = binsearch_seed_pos_reduce64(posp, buffer_p, reduce_pn - reduce_p, reduce_p, tid);
#else
b_r_s = binsearch_seed_pos_reduce(posp, buffer_p, reduce_pn - reduce_p, reduce_p, tid);
#endif
if(b_r_s != -1)
{
for(cov_i = 0; cov_i < cov_a_t; cov_i++)
(seedsets[tid][b_p_i].cov)[cov_i] |= (seed_tmp[seed_i].cov)[cov_i];
pos_add[tid][b_r_s - buffer_pp[uni_id]] = 1;
if(b_r_s == reduce_pn - 1)
break;
reduce_p = b_r_s + 1;
}
else
{
if(g_low[tid] == reduce_pn - reduce_p)
break;
else reduce_p += g_low[tid];
}
}
}
}
for(b_p_i = 0; b_p_i < bn; b_p_i++)
{
if(pos_add[tid][b_p_i] == 0)
{
seedsets[tid][set_n].seed_set = buffer_p[buffer_pp[uni_id] + b_p_i] + ref_off1 - r_p1;
memcpy(seedsets[tid][set_n].cov, seed_tmp[seed_i].cov, (cov_a_t) << 3);
seedsets[tid][set_n].ui = seed_tmp[seed_i].ui;
seedsets[tid][set_n].ref_pos_off = ref_off1;
seedsets[tid][set_n].ref_pos_off_r = seed_tmp[seed_i].ref_pos_off_r;
seedsets[tid][set_n].s_r_o_l = seed_tmp[seed_i].s_r_o_l;
seedsets[tid][set_n].s_r_o_r = seed_tmp[seed_i].s_r_o_r;
seedsets[tid][set_n].tid = tid;
++set_n;
}
}
memset(pos_add[tid], 0, bn);
seed_set_off[tid][seed_i + 1] = set_n;
++off_n;
}
#endif
for(off_i = 0; off_i < off_n - 1; off_i++)
{
interval_n = seed_set_off[tid][off_i + 1] - seed_set_off[tid][off_i];
if(interval_n == 0) continue;
qsort(seedsets[tid] + seed_set_off[tid][off_i], interval_n, sizeof(seed_sets), compare_sets);
//copy elements from seed_tmp[off_i] as for other elements such as quality
set_i_pre = seed_set_off[tid][off_i];
seedpa[spa_i].pos_start = set_i_pre;
memcpy(seedpa[spa_i].cov, seedsets[tid][set_i_pre].cov, (cov_a_t) << 3);
seedpa[spa_i].ref_pos_off = seedsets[tid][set_i_pre].ref_pos_off;
seedpa[spa_i].ref_pos_off_r = seedsets[tid][set_i_pre].ref_pos_off_r;
seedpa[spa_i].ui = seedsets[tid][set_i_pre].ui;
seedpa[spa_i].s_r_o_l = seedsets[tid][set_i_pre].s_r_o_l;
seedpa[spa_i].s_r_o_r = seedsets[tid][set_i_pre].s_r_o_r;
//cal number of 1 (length)
seedpa[spa_i].length = 0;
for(pop_i = 0; pop_i < cov_a_t; pop_i++)
seedpa[spa_i].length += popcount_3((seedpa[spa_i].cov)[pop_i]);
if(seedpa[spa_i].length > max_sets_n) max_sets_n = seedpa[spa_i].length;
++spa_i;
seed_same_n = 1;
//copy pos to seed_set_pos
(*seed_set_pos)[set_pos_n++] = seedsets[tid][set_i_pre].seed_set; //+ ref_off - r_p
for(set_i = set_i_pre + 1; set_i < seed_set_off[tid][off_i + 1]; set_i++)
{
set_c_r = memcmp(seedsets[tid][set_i_pre].cov, seedsets[tid][set_i].cov, (cov_a_t) << 3);
if(set_c_r != 0)
{
seedpa[spa_i - 1].pos_n = seed_same_n;
//copy elements from seed_tmp[off_i] as for other elements such as quality
seedpa[spa_i].pos_start = set_i;
memcpy(seedpa[spa_i].cov, seedsets[tid][set_i].cov, (cov_a_t) << 3);
seedpa[spa_i].ref_pos_off = seedsets[tid][set_i].ref_pos_off;
seedpa[spa_i].ref_pos_off_r = seedsets[tid][set_i].ref_pos_off_r;
seedpa[spa_i].ui = seedsets[tid][set_i].ui;
seedpa[spa_i].s_r_o_l = seedsets[tid][set_i].s_r_o_l;
seedpa[spa_i].s_r_o_r = seedsets[tid][set_i].s_r_o_r;
//cal number of 1 (length)
seedpa[spa_i].length = 0;
for(pop_i = 0; pop_i < cov_a_t; pop_i++)
seedpa[spa_i].length += popcount_3((seedpa[spa_i].cov)[pop_i]);
if(seedpa[spa_i].length > max_sets_n) max_sets_n = seedpa[spa_i].length;
++spa_i;
seed_same_n = 1;
}
else ++seed_same_n;
//copy pos to seed_set_pos
(*seed_set_pos)[set_pos_n++] = seedsets[tid][set_i].seed_set;// + ref_off - r_p
set_i_pre = set_i;
}
seedpa[spa_i - 1].pos_n = seed_same_n;
}
#ifdef SINGLE_COV_FILT
qsort(seedpa, spa_i, sizeof(seed_pa), compare_plen);
for(off_i = 0; off_i < spa_i; off_i++)
if(seedpa[off_i].length < max_sets_n - length_reduce)
{
++off_i;
break;
}
(*spa1_i) = off_i;
#else
(*spa1_i) = spa_i;
#endif
(*seed_num) = spa_i;
(*max_seed_length) = max_sets_n;
#ifdef PR_COV_FILTER
if(seed_l[tid] == COV_FIT_SI)
{
if(max_sets_n > (read_length >> 1)) cov_filt_f[tid] = 1;
}
#endif
return seedpa;
}
#ifdef UNPIPATH_OFF_K20
void merge_pair_end64(uint32_t spa1_i, uint32_t spa2_i, seed_pa* seed_pr1, seed_pa* seed_pr2, uint64_t* seed_set_pos1, uint64_t* seed_set_pos2, uint8_t rc_i, uint8_t tid)
#else
void merge_pair_end(uint32_t spa1_i, uint32_t spa2_i, seed_pa* seed_pr1, seed_pa* seed_pr2, uint32_t* seed_set_pos1, uint32_t* seed_set_pos2, uint8_t rc_i, uint8_t tid)
#endif
{
#ifdef UNPIPATH_OFF_K20
uint64_t posi = 0;
uint64_t posp = 0;
#else
uint32_t posi = 0;
uint32_t posp = 0;
#endif
//uint32_t pospi = 0;
uint32_t seed1_i = 0;
uint32_t seed2_i = 0;
uint32_t psp_i = 0;
uint32_t mat_posi1 = 0;
int64_t b_s_p_r_i = 0;
int64_t b_s_p_r = 0;
int64_t reduce_r = 0;
int64_t reduce_rn = 0;
uint16_t end_dis = 0;
if(rc_i == 0) end_dis = end_dis1[tid];
else end_dis = end_dis2[tid];
mat_posi1 = mat_posi[tid];
//match each side of pair-end read
for(seed1_i = 0; seed1_i < spa1_i; seed1_i++)
{
for(seed2_i = 0; seed2_i < spa2_i; seed2_i++)
{
#ifdef PAIR_B_R_V
if(seed_pr1[seed1_i].pos_n <= seed_pr2[seed2_i].pos_n)
{
reduce_r = seed_pr2[seed2_i].pos_start;
reduce_rn = seed_pr2[seed2_i].pos_n + seed_pr2[seed2_i].pos_start;
for(psp_i = 0; psp_i < seed_pr1[seed1_i].pos_n; psp_i++)
{
posi = seed_set_pos1[seed_pr1[seed1_i].pos_start + psp_i];
posp = posi + end_dis;
//can add if( != 0Xffffffff) in following binary search function
#ifdef UNPIPATH_OFF_K20
b_s_p_r = binsearch_pair_pos_reduce64(posp, seed_set_pos2, reduce_rn - reduce_r, reduce_r, tid);
#else
b_s_p_r = binsearch_pair_pos_reduce(posp, seed_set_pos2, reduce_rn - reduce_r, reduce_r, tid);
#endif
if(b_s_p_r != -1)
{
de_m_p[tid] = 0;
if(mat_posi1 < CUS_SEED_SET)
{
mat_pos1[tid][mat_posi1] = posi;
mat_pos2[tid][mat_posi1] = seed_set_pos2[b_s_p_r];
seed_no1[tid][mat_posi1] = seed1_i;
seed_no2[tid][mat_posi1] = seed2_i;
mat_rc[tid][mat_posi1] = rc_i;
++mat_posi1;
}
#ifdef PAIR_SEED_LENGTH_FILT
if(seed_pr1[seed1_i].length + seed_pr2[seed2_i].length > max_lengtht[tid])
max_lengtht[tid] = seed_pr1[seed1_i].length + seed_pr2[seed2_i].length;
#endif
if(b_s_p_r == reduce_rn - 1)
break;
#ifdef PAIR_TRAVERSE
for(b_s_p_r_i = b_s_p_r + 1; (seed_set_pos2[b_s_p_r_i] < posp + devi) && (b_s_p_r_i < reduce_rn); b_s_p_r_i++)
{
if(mat_posi1 < CUS_SEED_SET)
{
mat_pos1[tid][mat_posi1] = posi;
mat_pos2[tid][mat_posi1] = seed_set_pos2[b_s_p_r_i];
seed_no1[tid][mat_posi1] = seed1_i;
seed_no2[tid][mat_posi1] = seed2_i;
mat_rc[tid][mat_posi1] = rc_i;
++mat_posi1;
}
}
for(b_s_p_r_i = b_s_p_r - 1; (seed_set_pos2[b_s_p_r_i] > posp - devi) && (b_s_p_r_i >= reduce_r); b_s_p_r_i--)
{
if(mat_posi1 < CUS_SEED_SET)
{
mat_pos1[tid][mat_posi1] = posi;
mat_pos2[tid][mat_posi1] = seed_set_pos2[b_s_p_r_i];
seed_no1[tid][mat_posi1] = seed1_i;
seed_no2[tid][mat_posi1] = seed2_i;
mat_rc[tid][mat_posi1] = rc_i;
++mat_posi1;
}
}
#endif
reduce_r = b_s_p_r + 1;
}
else
{
if(r_low[tid] == reduce_rn - reduce_r)
break;
else reduce_r += r_low[tid];
}
}
}
else
{
reduce_r = seed_pr1[seed1_i].pos_start;
reduce_rn = seed_pr1[seed1_i].pos_n + seed_pr1[seed1_i].pos_start;
for(psp_i = 0; psp_i < seed_pr2[seed2_i].pos_n; psp_i++)
{
posi = seed_set_pos2[seed_pr2[seed2_i].pos_start + psp_i];
posp = posi - end_dis;
//can add if( != 0Xffffffff) in following binary search function
#ifdef UNPIPATH_OFF_K20
b_s_p_r = binsearch_pair_pos_reduce64(posp, seed_set_pos1, reduce_rn - reduce_r, reduce_r, tid);
#else
b_s_p_r = binsearch_pair_pos_reduce(posp, seed_set_pos1, reduce_rn - reduce_r, reduce_r, tid);
#endif
if(b_s_p_r != -1)
{
de_m_p[tid] = 0;
if(mat_posi1 < CUS_SEED_SET)
{
mat_pos1[tid][mat_posi1] = seed_set_pos1[b_s_p_r];
mat_pos2[tid][mat_posi1] = posi;
seed_no1[tid][mat_posi1] = seed1_i;
seed_no2[tid][mat_posi1] = seed2_i;
mat_rc[tid][mat_posi1] = rc_i;
++mat_posi1;
}
#ifdef PAIR_SEED_LENGTH_FILT
if(seed_pr1[seed1_i].length + seed_pr2[seed2_i].length > max_lengtht[tid])
max_lengtht[tid] = seed_pr1[seed1_i].length + seed_pr2[seed2_i].length;
#endif
if(b_s_p_r == reduce_rn - 1)
break;
#ifdef PAIR_TRAVERSE
for(b_s_p_r_i = b_s_p_r + 1; (seed_set_pos1[b_s_p_r_i] < posp + devi) && (b_s_p_r_i < reduce_rn); b_s_p_r_i++)
{
if(mat_posi1 < CUS_SEED_SET)
{
#ifdef MERGE_MODIFY
mat_pos1[tid][mat_posi1] = seed_set_pos1[b_s_p_r_i];
mat_pos2[tid][mat_posi1] = posi;
#else
mat_pos1[tid][mat_posi1] = posi;
mat_pos2[tid][mat_posi1] = seed_set_pos1[b_s_p_r_i];
#endif
seed_no1[tid][mat_posi1] = seed1_i;
seed_no2[tid][mat_posi1] = seed2_i;
mat_rc[tid][mat_posi1] = rc_i;
++mat_posi1;
}
}
for(b_s_p_r_i = b_s_p_r - 1; (seed_set_pos1[b_s_p_r_i] > posp - devi) && (b_s_p_r_i >= reduce_r); b_s_p_r_i--)
{
if(mat_posi1 < CUS_SEED_SET)
{
#ifdef MERGE_MODIFY
mat_pos1[tid][mat_posi1] = seed_set_pos1[b_s_p_r_i];
mat_pos2[tid][mat_posi1] = posi;
#else
mat_pos1[tid][mat_posi1] = posi;
mat_pos2[tid][mat_posi1] = seed_set_pos1[b_s_p_r_i];
#endif
seed_no1[tid][mat_posi1] = seed1_i;
seed_no2[tid][mat_posi1] = seed2_i;
mat_rc[tid][mat_posi1] = rc_i;
++mat_posi1;
}
}
#endif
reduce_r = b_s_p_r + 1;
}
else
{
if(r_low[tid] == reduce_rn - reduce_r)
break;
else reduce_r += r_low[tid];
}
}
}
#endif
}
}
mat_posi[tid] = mat_posi1;
}
void pair_sam_output(uint8_t tid, uint16_t read_length1, uint16_t read_length2, uint16_t f_cigarn, cnt_re* cnt, uint32_t seqi, uint16_t lv_k1, uint16_t lv_k2, int16_t pound_pos1_f_forward, int16_t pound_pos1_f_reverse, int16_t pound_pos1_r_forward, int16_t pound_pos1_r_reverse, int16_t pound_pos2_f_forward, int16_t pound_pos2_f_reverse, int16_t pound_pos2_r_forward, int16_t pound_pos2_r_reverse, uint8_t cir_n)
{
//alignment in optimal and suboptimal vectors and output to sam file
uint8_t sam_flag1 = 0;
uint8_t sam_flag2 = 0;
uint16_t v_cnt_out = 0;
uint16_t vs_cnt_out = 0;
uint16_t d_n1 = 0;
uint16_t d_n2 = 0;
uint16_t i_n1 = 0;
uint16_t i_n2 = 0;
uint16_t f_c = 0;
uint16_t pchl = 0;
uint16_t f_i = 0;
uint16_t s_o = 0;
uint16_t sn = 0;
uint16_t snt = 0;
uint16_t read_b_i = 0;
uint16_t sam_seq_i = 0;
uint16_t xa_i = 0;
uint16_t xa_i1 = 0;
uint16_t xa_i2 = 0;
uint16_t v_cnt_i = 0;
uint16_t va_cnt_i = 0;
uint32_t v_cnt = 0;
uint32_t vs_cnt = 0;
int low = 0;
int high = 0;
int mid = 0;
int chr_re = 0;
int bit_char_i = 0;
int lv_re1f = 0;
int lv_re1b = 0;
int lv_re2f = 0;
int lv_re2b = 0;
int lv_re1 = 0;
int lv_re2 = 0;
int sam_qual1 = 0;
int sam_qual2 = 0;
int m_m_n = 0;
int16_t m_n_f = 0;
int16_t m_n_b = 0;
int16_t s_r_o_l = 0;
int16_t s_r_o_r = 0;
int16_t lv_up_left = 0;
int16_t lv_up_right = 0;
int16_t lv_down_right = 0;
int16_t lv_down_left = 0;
int16_t pound_pos_1_f = 0;
int16_t pound_pos_1_r = 0;
int16_t pound_pos_2_f = 0;
int16_t pound_pos_2_r = 0;
int64_t sam_pos1 = 0;
int64_t sam_pos2 = 0;
int64_t sam_cross = 0;
int64_t sam_pos1_pr = 0;
int64_t sam_pos2_pr = 0;
uint8_t rc_i = 0;
uint8_t rc_ii = 0;
char sam_seq1[MAX_READLEN] = {};
char sam_seq2[MAX_READLEN] = {};
char cigarBuf1[MAX_LV_CIGAR] = {};
char cigarBuf2[MAX_LV_CIGAR] = {};
uint16_t f_cigar[MAX_LV_CIGAR];
char str_o[MAX_LV_CIGAR];
char b_cigar[MAX_LV_CIGAR];
char* pch = NULL;
char* saveptr = NULL;
#ifdef KSW_ALN_PAIR
int band_with = 33;//100
int x_score, y_score, op_score, len_score, op_score1, len_score1, op_score2, len_score2;
int k_start1 = 0;
int k_start2 = 0;
int k_middle = 0;
uint32_t* cigar1 = NULL;
uint32_t* cigar2 = NULL;
int n_cigar1 = 0;
int n_cigar2 = 0;
int nm_score = 0;
#endif
#ifdef QUAL_FILT_LV_OUT
uint8_t* qual_filt_lv_1 = NULL;
uint8_t* qual_filt_lv_1_o = NULL;
uint8_t* qual_filt_lv_2 = NULL;
uint8_t* qual_filt_lv_2_o = NULL;
#endif
char cigar_p1[MAX_LV_CIGARCOM];
char cigar_p2[MAX_LV_CIGARCOM];
uint16_t s_offset1 = 0;
uint16_t s_offset2 = 0;
#ifdef MAPPING_QUALITY
float log_tmp = 0;
float* mp_subs_1 = NULL;
float* mp_subs_1_o = NULL;
float* mp_subs_2 = NULL;
float* mp_subs_2_o = NULL;
uint8_t mp_flag = 0;
#endif
uint8_t ops_flag = 1;
#ifdef UNPIPATH_OFF_K20
uint64_t x = 0;
#else
uint32_t x = 0;
#endif
uint64_t chr_re_tmp = 0;
v_cnt = cnt->v_cnt;
vs_cnt = cnt->vs_cnt;
v_cnt_out = (cus_ali_n < v_cnt) ? cus_ali_n:v_cnt;
v_cnt_i = 0;
#ifdef CIGAR_LEN_ERR
int cigar_len = 0;
int cigar_len_tmp = 0;
int cigar_len_re = 0;
uint16_t pchl_tmp = 0;
uint16_t s_o_tmp = 0;
char* pch_tmp = NULL;
char* saveptr_tmp = NULL;
char cigar_tmp[MAX_LV_CIGARCOM];
#endif
#ifdef ALTER_DEBUG
if((v_cnt > 1) && (rep_go[tid])) v_cnt_i = seed_length_arr[tid][v_cnt_i].index;
#endif
#ifdef MAPPING_QUALITY
if(v_cnt > 1)
{
sam_qual1 = 0;
sam_qual2 = 0;
mp_flag = 0;
}
else if(vs_cnt == 0)
{
sam_qual1 = 60;
sam_qual2 = 60;
mp_flag = 0;
}
else
{
mp_flag = 1;
}
#endif
x = op_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos1 = op_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
sam_pos2 = op_vector_pos2[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
if(op_rc[tid][v_cnt_i] == 0)
{
sam_flag1 = 99;
sam_flag2 = 147;
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
strcpy(sam_seq1, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_LV_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
qual_filt_lv_2 = qual_filt_lv2[tid][1];
qual_filt_lv_2_o = qual_filt_lv2[tid][0];
#endif
sam_cross = sam_pos2 + read_length2 - sam_pos1;
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
#ifdef MAPPING_QUALITY
if(mp_flag)
{
mp_subs_1 = mp_subs1[tid][0];
mp_subs_1_o = mp_subs1[tid][1];
mp_subs_2 = mp_subs2[tid][1];
mp_subs_2_o = mp_subs2[tid][0];
}
#endif
}
else
{
sam_flag1 = 83;
sam_flag2 = 163;
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#ifdef QUAL_FILT_LV_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
qual_filt_lv_2 = qual_filt_lv2[tid][0];
qual_filt_lv_2_o = qual_filt_lv2[tid][1];
#endif
sam_cross = sam_pos2 - read_length1 - sam_pos1;
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
#ifdef MAPPING_QUALITY
if(mp_flag)
{
mp_subs_1 = mp_subs1[tid][1];
mp_subs_1_o = mp_subs1[tid][0];
mp_subs_2 = mp_subs2[tid][0];
mp_subs_2_o = mp_subs2[tid][1];
}
#endif
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = op_dm_l1[tid][v_cnt_i];
s_r_o_r = op_dm_r1[tid][v_cnt_i];
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] = 0;
#endif
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m1[tid]);
#ifdef MAPPING_QUALITY
if(mp_flag)
{
for (bit_char_i = 0, read_b_i = 32; bit_char_i < read_length1; bit_char_i++, read_b_i++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((op_vector_seq1[tid][v_cnt_i][read_b_i >> 5] >> ((31 - (read_b_i & 0X1f)) << 1)) & 0X3))
{
sub_t[tid] += mp_subs_1[bit_char_i];
}
}
#endif
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
#ifdef CHAR_CP
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kl1[tid][v_cnt_i], read_char[tid], op_dm_kl1[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr1[tid][v_cnt_i], read_char2[tid], op_dm_kr1[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if (n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if (n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if (s_r_o_l >= op_dm_kl1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", s_r_o_l + 1 - op_dm_kl1[tid][v_cnt_i]);
snt += sn;
}
if ((s_r_o_l != -1) && (s_r_o_r != read_length1))
{
if ((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if (op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if (op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_1_o[read_length1 + n_cigar1 - s_r_o_l - x_score - read_b_i - 2];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if (s_r_o_l == -1)
{
if (op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if (op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_1_o[read_length1 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
}
if (read_length1 - s_r_o_r > op_dm_kr1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", read_length1 - s_r_o_r - op_dm_kr1[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
if (n_cigar1) free(cigar1);
if (n_cigar2) free(cigar2);
op_dm_ex1[tid][v_cnt_i] = nm_score;
#endif
}
else
{
if(pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if(pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_LV_OUT
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mis_left_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1, mp_subs_1_o + read_length1 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mis_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left, mp_subs_1 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#else
#ifdef CHAR_CP
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], mp_subs_1_o + read_length1 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], mp_subs_1 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p1 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if(m_n_f)
{
if(f_c)
{
if(f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left)) //(op_dm_l1[tid][v_cnt_i] != -1) && (op_dm_r1[tid][v_cnt_i] != read_length1)
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if(b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length1)
{
sn = sprintf(cigar_p1 + snt, "%uS", read_length1 - lv_down_right);
snt += sn;
}
#else
if(m_n_b)
{
if(cigar_p1[snt - 1] == 'M')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p1[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
//sprintf(cigar_p1 + snt, "\0");
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length1 != cigar_len)
{
if(read_length1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length1);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m1[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length1 - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
}
d_n2 = 0;
i_n2 = 0;
s_r_o_l = op_dm_l2[tid][v_cnt_i];
s_r_o_r = op_dm_r2[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m2[tid]);
#ifdef MAPPING_QUALITY
if(mp_flag)
{
for (bit_char_i = 0, read_b_i = 32; bit_char_i < read_length2; bit_char_i++, read_b_i++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((op_vector_seq2[tid][v_cnt_i][read_b_i >> 5] >> ((31 - (read_b_i & 0X1f)) << 1)) & 0X3))
{
sub_t[tid] += mp_subs_2[bit_char_i];
}
}
#endif
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
#ifdef CHAR_CP
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq2[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kl2[tid][v_cnt_i], read_char[tid], op_dm_kl2[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq2[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr2[tid][v_cnt_i], read_char2[tid], op_dm_kr2[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if (n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if (n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if (s_r_o_l >= op_dm_kl2[tid][v_cnt_i])
{
sn = sprintf(cigar_p2 + snt, "%dS", s_r_o_l + 1 - op_dm_kl2[tid][v_cnt_i]);
snt += sn;
}
if ((s_r_o_l != -1) && (s_r_o_r != read_length2))
{
if ((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if (op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if (op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_2_o[read_length2 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_2[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if (s_r_o_l == -1)
{
if (op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_2[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if (op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if(mp_flag) sub_t[tid] += mp_subs_2_o[read_length2 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
}
if (read_length2 - s_r_o_r > op_dm_kr2[tid][v_cnt_i])
{
sn = sprintf(cigar_p2 + snt, "%dS", read_length2 - s_r_o_r - op_dm_kr2[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p2 + snt, "\0");
//snt += sn;
if (n_cigar1) free(cigar1);
if (n_cigar2) free(cigar2);
op_dm_ex2[tid][v_cnt_i] = nm_score;
#endif
}
else
{
#ifdef OUTPUT_DEBUG
if (pound_pos_2_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_2_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length2 - pound_pos_2_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if (pound_pos_2_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_2_r;//21
lv_up_right = s_r_o_l;//20
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_2_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if ((pound_pos_2_f <= s_r_o_l + 1) && (pound_pos_2_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_2_f - 1;
lv_down_right = read_length2;
lv_down_left = pound_pos_2_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_2_r - pound_pos_2_f;
}
else if ((pound_pos_2_f > s_r_o_l + 1) && (pound_pos_2_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = pound_pos_2_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length2 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_LV_OUT
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mis_left_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2, mp_subs_2_o + read_length2 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mis_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left, mp_subs_2 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#else
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], mp_subs_2_o + read_length2 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if(mp_flag)
computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], mp_subs_2 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
#endif
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if (str_o[s_o - 1] == 'D') d_n2 += atoi(pch);
if (str_o[s_o - 1] == 'I') i_n2 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if (pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if (m_n_f)
{
if(f_c)
{
if (f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if ((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left))
{
if ((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if (b_cigar[pchl] == 'M')
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if (b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length2)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length2 - lv_down_right);
snt += sn;
}
#else
if (m_n_b)
{
if (cigar_p2[snt - 1] == 'M')
{
for (bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if ((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
//sprintf(cigar_p2 + snt, "\0");
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length2 != cigar_len)
{
if(read_length2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m2[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
#ifdef MAPPING_QUALITY
if(mp_flag)
{
sam_qual1 = sub_t[tid];
}
#endif
sam_pos1_pr = sam_pos1 + i_n1 - d_n1 + s_offset1;
sam_pos2_pr = sam_pos2 + i_n2 - d_n2 + s_offset2;
chr_re_tmp = chr_end_n[chr_re] - chr_end_n[chr_re - 1];
if(sam_pos1_pr <= 0)
{
sam_pos1_pr = 1;
}
else
{
if((sam_pos1_pr + read_length1 - 1) > chr_re_tmp)
sam_pos1_pr = chr_re_tmp - 1 - read_length1;
}
if(sam_pos2_pr <= 0)
{
sam_pos2_pr = 1;
}
else
{
if((sam_pos2_pr + read_length2 - 1) > chr_re_tmp)
sam_pos2_pr = chr_re_tmp - 1 - read_length2;
}
#ifdef OUTPUT_ARR
seqio[seqi].flag1 = sam_flag1;
seqio[seqi].flag2 = sam_flag2;
//seqio[seqi].chr_re = chr_re;
seqio[seqi].chr_re1 = chr_re;
seqio[seqi].chr_re2 = chr_re;
seqio[seqi].pos1 = sam_pos1_pr;
seqio[seqi].pos2 = sam_pos2_pr;
seqio[seqi].cross = sam_cross;
seqio[seqi].nm1 = op_dm_ex1[tid][v_cnt_i];
seqio[seqi].nm2 = op_dm_ex2[tid][v_cnt_i];
strcpy(pr_cigar1_buffer[seqi], cigar_p1);
seqio[seqi].cigar1 = pr_cigar1_buffer[seqi];
strcpy(pr_cigar2_buffer[seqi], cigar_p2);
seqio[seqi].cigar2 = pr_cigar2_buffer[seqi];
if(sam_flag1 == 99)
{
#ifdef CHAR_CP
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
#endif
strcpy(read_rev_buffer[seqi], sam_seq2);
read_rev_buffer[seqi][read_length2] = '\0';
seqio[seqi].seq2 = read_rev_buffer[seqi];
seqio[seqi].seq1 = seqio[seqi].read_seq1;
strrev1(qual2_buffer[seqi]);
seqio[seqi].qual1 = qual1_buffer[seqi];
seqio[seqi].qual2 = qual2_buffer[seqi];
}
else
{
#ifdef CHAR_CP
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#endif
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length1] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
seqio[seqi].seq2 = seqio[seqi].read_seq2;
strrev1(qual1_buffer[seqi]);
seqio[seqi].qual1 = qual1_buffer[seqi];
seqio[seqi].qual2 = qual2_buffer[seqi];
}
#endif
//}
xa_i = 0;
for(va_cnt_i = 1; va_cnt_i < v_cnt_out; va_cnt_i++)
{
#ifdef ALTER_DEBUG
if(rep_go[tid]) v_cnt_i = seed_length_arr[tid][va_cnt_i].index;
else v_cnt_i = va_cnt_i;
#else
v_cnt_i = va_cnt_i;
#endif
x = op_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos1 = op_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
sam_pos2 = op_vector_pos2[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
chr_res[tid][xa_i] = chr_re;
if(op_rc[tid][v_cnt_i] == 0)
{
#ifdef OUPUT_REPEAT
sam_flag1 = 99;
sam_flag2 = 147;
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
strcpy(sam_seq1, seqio[seqi].read_seq1);
#endif
#endif
#ifdef QUAL_FILT_LV_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
qual_filt_lv_2 = qual_filt_lv2[tid][1];
qual_filt_lv_2_o = qual_filt_lv2[tid][0];
#endif
sam_cross = sam_pos2 + read_length2 - sam_pos1;
xa_d1s[tid][xa_i] = '+';
xa_d2s[tid][xa_i] = '-';
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
}
else
{
#ifdef OUPUT_REPEAT
sam_flag1 = 83;
sam_flag2 = 163;
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#endif
#ifdef QUAL_FILT_LV_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
qual_filt_lv_2 = qual_filt_lv2[tid][0];
qual_filt_lv_2_o = qual_filt_lv2[tid][1];
#endif
sam_cross = sam_pos2 - read_length1 - sam_pos1;
xa_d1s[tid][xa_i] = '-';
xa_d2s[tid][xa_i] = '+';
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = op_dm_l1[tid][v_cnt_i];
s_r_o_r = op_dm_r1[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m1[tid]);
lv_re1 = op_dm_ex1[tid][v_cnt_i];
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
#ifdef CHAR_CP
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kl1[tid][v_cnt_i], read_char[tid], op_dm_kl1[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr1[tid][v_cnt_i], read_char2[tid], op_dm_kr1[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if (n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if (n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if (s_r_o_l >= op_dm_kl1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", s_r_o_l + 1 - op_dm_kl1[tid][v_cnt_i]);
snt += sn;
}
if ((s_r_o_l != -1) && (s_r_o_r != read_length1))
{
if ((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if (op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if (op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if (s_r_o_l == -1)
{
if (op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if (op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
}
if (read_length1 - s_r_o_r > op_dm_kr1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", read_length1 - s_r_o_r - op_dm_kr1[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
if (n_cigar1) free(cigar1);
if (n_cigar2) free(cigar2);
lv_re1 = nm_score;
#endif
}
else
{
#ifdef OUTPUT_DEBUG
if (pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if (pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if ((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if ((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_LV_OUT
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re1f = computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re1b = computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re1f = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re1b = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
lv_re1 = lv_re1f + lv_re1b;
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if (str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if (str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if (pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p1 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if (m_n_f)
{
if(f_c)
{
if (f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if ((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left))
{
if ((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if (b_cigar[pchl] == 'M')
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if (b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length1)
{
sn = sprintf(cigar_p1 + snt, "%uS", read_length1 - lv_down_right);
snt += sn;
}
#else
if (m_n_b)
{
if (cigar_p1[snt - 1] == 'M')
{
for (bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if ((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p1[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
//sprintf(cigar_p1 + snt, "\0");
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length1 != cigar_len)
{
if(read_length1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length1);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m1[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length1 - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
}
d_n2 = 0;
i_n2 = 0;
s_r_o_l = op_dm_l2[tid][v_cnt_i];
s_r_o_r = op_dm_r2[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m2[tid]);
lv_re2 = op_dm_ex2[tid][v_cnt_i];
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
#ifdef CHAR_CP
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq2[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kl2[tid][v_cnt_i], read_char[tid], op_dm_kl2[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq2[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr2[tid][v_cnt_i], read_char2[tid], op_dm_kr2[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if (n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if (n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if (s_r_o_l >= op_dm_kl2[tid][v_cnt_i])
{
sn = sprintf(cigar_p2 + snt, "%dS", s_r_o_l + 1 - op_dm_kl2[tid][v_cnt_i]);
snt += sn;
}
if ((s_r_o_l != -1) && (s_r_o_r != read_length2))
{
if ((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if (op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if (op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if (s_r_o_l == -1)
{
if (op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if (op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
}
if (read_length2 - s_r_o_r > op_dm_kr2[tid][v_cnt_i])
{
sn = sprintf(cigar_p2 + snt, "%dS", read_length2 - s_r_o_r - op_dm_kr2[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p2 + snt, "\0");
//snt += sn;
if (n_cigar1) free(cigar1);
if (n_cigar2) free(cigar2);
lv_re2 = nm_score;
#endif
}
else
{
#ifdef OUTPUT_DEBUG
if (pound_pos_2_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_2_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length2 - pound_pos_2_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if (pound_pos_2_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_2_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_2_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if ((pound_pos_2_f <= s_r_o_l + 1) && (pound_pos_2_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_2_f - 1;
lv_down_right = read_length2;
lv_down_left = pound_pos_2_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_2_r - pound_pos_2_f;
}
else if ((pound_pos_2_f > s_r_o_l + 1) && (pound_pos_2_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = pound_pos_2_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length2 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_LV_OUT
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re2f = computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re2b = computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re2f = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
lv_re2b = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
lv_re2 = lv_re2f + lv_re2b;
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if (str_o[s_o - 1] == 'D') d_n2 += atoi(pch);
if (str_o[s_o - 1] == 'I') i_n2 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if (pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if (m_n_f)
{
if(f_c)
{
if (f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if ((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left))
{
if ((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if (b_cigar[pchl] == 'M')
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if (b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length2)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length2 - lv_down_right);
snt += sn;
}
#else
if (m_n_b)
{
if (cigar_p2[snt - 1] == 'M')
{
for (bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if ((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
//sprintf(cigar_p2 + snt, "\0");
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length2 != cigar_len)
{
if(read_length2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m2[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
sam_pos1s[tid][xa_i] = (uint32_t )(sam_pos1 + i_n1 - d_n1 + s_offset1);
sam_pos2s[tid][xa_i] = (uint32_t )(sam_pos2 + i_n2 - d_n2 + s_offset2);
strcpy(cigar_p1s[tid][xa_i], cigar_p1);
strcpy(cigar_p2s[tid][xa_i], cigar_p2);
lv_re1s[tid][xa_i] = lv_re1;
lv_re2s[tid][xa_i] = lv_re2;
++xa_i;
}
//suboptimal
vs_cnt_out = (cus_ali_n < vs_cnt) ? cus_ali_n:vs_cnt;
#ifdef ALL_ALL
for(v_cnt_i = 0; v_cnt_i < vs_cnt_out; v_cnt_i++)
#else
if((mgn_flag) && (v_cnt_out > 1))
ops_flag = 0;
for(v_cnt_i = 0; (v_cnt_i < vs_cnt_out) && (dm_op[tid] + 3 > dm_ops[tid]) && ops_flag; v_cnt_i++)// && (v_cnt_out < 2)
#endif
{
x = ops_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos1 = ops_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
sam_pos2 = ops_vector_pos2[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
chr_res[tid][xa_i] = chr_re;
if(ops_rc[tid][v_cnt_i] == 0)
{
#ifdef OUPUT_REPEAT
sam_flag1 = 99;
sam_flag2 = 147;
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][0];
read_bit_2[tid] = read_bit2[tid][1];
#else
for(sam_seq_i = 0; sam_seq_i < read_length2; sam_seq_i++)
sam_seq2[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq2[sam_seq_i]] ^ 0X3];
sam_seq2[sam_seq_i] = '\0';
strrev1(sam_seq2);
strcpy(sam_seq1, seqio[seqi].read_seq1);
#endif
#endif
#ifdef QUAL_FILT_LV_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
qual_filt_lv_2 = qual_filt_lv2[tid][1];
qual_filt_lv_2_o = qual_filt_lv2[tid][0];
#endif
sam_cross = sam_pos2 + read_length2 - sam_pos1;
xa_d1s[tid][xa_i] = '+';
xa_d2s[tid][xa_i] = '-';
pound_pos_1_f = pound_pos1_f_forward;
pound_pos_1_r = pound_pos1_r_forward;
pound_pos_2_f = pound_pos2_f_reverse;
pound_pos_2_r = pound_pos2_r_reverse;
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
{
mp_subs_1 = mp_subs1[tid][0];
mp_subs_1_o = mp_subs1[tid][1];
mp_subs_2 = mp_subs2[tid][1];
mp_subs_2_o = mp_subs2[tid][0];
}
#endif
}
else
{
#ifdef OUPUT_REPEAT
sam_flag1 = 83;
sam_flag2 = 163;
#ifdef CHAR_CP
read_bit_1[tid] = read_bit1[tid][1];
read_bit_2[tid] = read_bit2[tid][0];
#else
for(sam_seq_i = 0; sam_seq_i < read_length1; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
strcpy(sam_seq2, seqio[seqi].read_seq2);
#endif
#endif
#ifdef QUAL_FILT_LV_OUT
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
qual_filt_lv_2 = qual_filt_lv2[tid][0];
qual_filt_lv_2_o = qual_filt_lv2[tid][1];
#endif
sam_cross = sam_pos2 - read_length1 - sam_pos1;
xa_d1s[tid][xa_i] = '-';
xa_d2s[tid][xa_i] = '+';
pound_pos_1_f = pound_pos1_f_reverse;
pound_pos_1_r = pound_pos1_r_reverse;
pound_pos_2_f = pound_pos2_f_forward;
pound_pos_2_r = pound_pos2_r_forward;
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
{
mp_subs_1 = mp_subs1[tid][1];
mp_subs_1_o = mp_subs1[tid][0];
mp_subs_2 = mp_subs2[tid][0];
mp_subs_2_o = mp_subs2[tid][1];
}
#endif
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_offset2 = 0;
s_r_o_l = ops_dm_l1[tid][v_cnt_i];
s_r_o_r = ops_dm_r1[tid][v_cnt_i];
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] = 0;
#endif
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m1[tid]);
lv_re1 = ops_dm_ex1[tid][v_cnt_i];
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
{
for (bit_char_i = 0, read_b_i = 32; bit_char_i < read_length1; bit_char_i++, read_b_i++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ops_vector_seq1[tid][v_cnt_i][read_b_i >> 5] >> ((31 - (read_b_i & 0X1f)) << 1)) & 0X3))
{
sub_t[tid] += mp_subs_1[bit_char_i];
}
}
#endif
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
#ifdef CHAR_CP
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(ops_dm_kl1[tid][v_cnt_i], read_char[tid], ops_dm_kl1[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(ops_dm_kr1[tid][v_cnt_i], read_char2[tid], ops_dm_kr1[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if (n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if (n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if (s_r_o_l >= ops_dm_kl1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", s_r_o_l + 1 - ops_dm_kl1[tid][v_cnt_i]);
snt += sn;
}
if ((s_r_o_l != -1) && (s_r_o_r != read_length1))
{
if ((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if (op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if (op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1_o[read_length1 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if (s_r_o_l == -1)
{
if (op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if (op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1_o[read_length1 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
}
if (read_length1 - s_r_o_r > ops_dm_kr1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", read_length1 - s_r_o_r - ops_dm_kr1[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
if (n_cigar1) free(cigar1);
if (n_cigar2) free(cigar2);
lv_re1 = nm_score;
#endif
}
else
{
#ifdef OUTPUT_DEBUG
if (pound_pos_1_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_1_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length1 - pound_pos_1_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if (pound_pos_1_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_1_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_1_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if ((pound_pos_1_f <= s_r_o_l + 1) && (pound_pos_1_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_1_f - 1;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_1_r - pound_pos_1_f;
}
else if ((pound_pos_1_f > s_r_o_l + 1) && (pound_pos_1_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length1;
lv_down_left = pound_pos_1_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length1 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length1;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_LV_OUT
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re1f = computeEditDistanceWithCigar_s_mis_left_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1, mp_subs_1_o + read_length1 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
lv_re1f = computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
lv_re1f = computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length1 - 1 - lv_up_right, &s_offset1);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re1b = computeEditDistanceWithCigar_s_mis_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left, mp_subs_1 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else
lv_re1b = computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
lv_re1b = computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#else
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re1f = computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid], mp_subs_1_o + read_length1 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
lv_re1f = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
lv_re1f = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k1, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re1b = computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid], mp_subs_1 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else
lv_re1b = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
lv_re1b = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k1, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
#endif
lv_re1 = lv_re1f + lv_re1b;
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if (str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if (str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if (pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p1 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if (m_n_f)
{
if(f_c)
{
if (f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if ((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left))
{
if ((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if (b_cigar[pchl] == 'M')
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if (b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length1)
{
sn = sprintf(cigar_p1 + snt, "%uS", read_length1 - lv_down_right);
snt += sn;
}
#else
if (m_n_b)
{
if (cigar_p1[snt - 1] == 'M')
{
for (bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if ((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p1[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p1[bit_char_i] > 64) && (cigar_p1[bit_char_i] < 91)) break;
m_n_b += (cigar_p1[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p1 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p1 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
//sprintf(cigar_p1 + snt, "\0");
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length1 != cigar_len)
{
if(read_length1 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length1);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m1[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length1 - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
}
d_n2 = 0;
i_n2 = 0;
s_r_o_l = ops_dm_l2[tid][v_cnt_i];
s_r_o_r = ops_dm_r2[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p2, cigar_m2[tid]);
lv_re2 = ops_dm_ex2[tid][v_cnt_i];
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
{
for (bit_char_i = 0, read_b_i = 32; bit_char_i < read_length2; bit_char_i++, read_b_i++)
if(((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ops_vector_seq2[tid][v_cnt_i][read_b_i >> 5] >> ((31 - (read_b_i & 0X1f)) << 1)) & 0X3))
{
sub_t[tid] += mp_subs_2[bit_char_i];
}
}
#endif
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN_PAIR
#ifdef CHAR_CP
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = charToDna5n[sam_seq2[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl2[tid][v_cnt_i]; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(ops_dm_kl2[tid][v_cnt_i], read_char[tid], ops_dm_kl2[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)
read_char2[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)
read_char2[tid][read_b_i] = charToDna5n[sam_seq2[bit_char_i]];
#endif
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr2[tid][v_cnt_i]; bit_char_i++, read_b_i++)
ali_ref_seq2[tid][read_b_i] = ((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(ops_dm_kr2[tid][v_cnt_i], read_char2[tid], ops_dm_kr2[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if (n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if (n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if (s_r_o_l >= ops_dm_kl2[tid][v_cnt_i])
{
sn = sprintf(cigar_p2 + snt, "%dS", s_r_o_l + 1 - ops_dm_kl2[tid][v_cnt_i]);
snt += sn;
}
if ((s_r_o_l != -1) && (s_r_o_r != read_length2))
{
if ((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if (op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if (op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_2_o[read_length2 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_2[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if (s_r_o_l == -1)
{
if (op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_2[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if (op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p2 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0)
{
// match
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_2_o[read_length2 + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p2 + snt, "%dM", k_middle);
snt += sn;
}
if (read_length2 - s_r_o_r > ops_dm_kr2[tid][v_cnt_i])
{
sn = sprintf(cigar_p2 + snt, "%dS", read_length2 - s_r_o_r - ops_dm_kr2[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p2 + snt, "\0");
//snt += sn;
if (n_cigar1) free(cigar1);
if (n_cigar2) free(cigar2);
lv_re2 = nm_score;
#endif
}
else
{
#ifdef OUTPUT_DEBUG
if (pound_pos_2_f >= s_r_o_r) //1
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = pound_pos_2_f;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = read_length2 - pound_pos_2_f;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if (pound_pos_2_r <= s_r_o_l + 1) //5
{
lv_up_left = pound_pos_2_r;//
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = pound_pos_2_r;
m_n_b = 0;
m_m_n = s_r_o_r - s_r_o_l - 1;
}
else if ((pound_pos_2_f <= s_r_o_l + 1) && (pound_pos_2_r >= s_r_o_r)) //2
{
lv_up_left = 0;
lv_up_right = pound_pos_2_f - 1;
lv_down_right = read_length2;
lv_down_left = pound_pos_2_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = pound_pos_2_r - pound_pos_2_f;
}
else if ((pound_pos_2_f > s_r_o_l + 1) && (pound_pos_2_f < s_r_o_r)) //3
{
lv_up_left = 0;
lv_up_right = s_r_o_l;
lv_down_right = read_length2;
lv_down_left = pound_pos_2_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = read_length2 - s_r_o_l - 1;
}
else //4
{
lv_up_left = 0;
lv_up_right = -1;
lv_down_right = read_length2;
lv_down_left = s_r_o_r;
m_n_f = 0;
m_n_b = 0;
m_m_n = s_r_o_r;
}
#ifdef QUAL_FILT_LV_OUT
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re2f = computeEditDistanceWithCigar_s_mis_left_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2, mp_subs_2_o + read_length2 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
lv_re2f = computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
lv_re2f = computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_2_o + read_length2 - 1 - lv_up_right, &s_offset2);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re2b = computeEditDistanceWithCigar_s_mis_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left, mp_subs_2 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else
lv_re2b = computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
lv_re2b = computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_2 + lv_down_left);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#else
#ifdef CHAR_CP
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_up_right, read_b_i = 0; bit_char_i >= lv_up_left; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_up_right, read_b_i = 0; bit_char_i > lv_up_left - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re2f = computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid], mp_subs_2_o + read_length2 - 1 - lv_up_right, &(sub_t[tid]));//, 0, op_dm_sl1[tid][v_cnt_i]
else
lv_re2f = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#else
lv_re2f = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + lv_up_right - lv_up_left, read_char[tid], lv_up_right + 1 - lv_up_left, lv_k2, cigarBuf1, f_cigarn, L[tid]);//, 0, op_dm_sl1[tid][v_cnt_i]
#endif
#ifdef CHAR_CP
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_2[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for (bit_char_i = lv_down_left, read_b_i = 0; bit_char_i < lv_down_right; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq2[bit_char_i];
for (bit_char_i = 32 + lv_down_left, read_b_i = 0; bit_char_i < lv_down_right + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq2[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY
if((mp_flag) && (v_cnt_i == 0))
lv_re2b = computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid], mp_subs_2 + lv_down_left, &(sub_t[tid]));//, 0, op_dm_sr1[tid][v_cnt_i]
else
lv_re2b = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#else
lv_re2b = computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + lv_down_right - lv_down_left, read_char[tid], lv_down_right - lv_down_left, lv_k2, cigarBuf2, f_cigarn, L[tid]);//, 0, op_dm_sr1[tid][v_cnt_i]
#endif
#endif
#endif
lv_re2 = lv_re2f + lv_re2b;
//deal with front and back lv cigar
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if (str_o[s_o - 1] == 'D') d_n2 += atoi(pch);
if (str_o[s_o - 1] == 'I') i_n2 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok(cigarBuf2,"DMIS");
if (pch != NULL)
pchl = strlen(pch);
snt = 0;
#ifdef CIGAR_S_MODIFY
if(lv_up_left)
{
sn = sprintf(cigar_p2 + snt, "%uS", lv_up_left);
snt += sn;
}
#else
if (m_n_f)
{
if(f_c)
{
if (f_cigar[f_cigarn + 1 - f_c] == 'M')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else if(f_cigar[f_cigarn + 1 - f_c] == 'S')
{
f_cigar[f_cigarn - f_c] += m_n_f;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_f);
snt += sn;
}
}
else m_m_n += m_n_f;
}
#endif
if ((lv_up_right >= lv_up_left) && (lv_down_right > lv_down_left))
{
if ((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%s",b_cigar);
snt += sn;
}
else if (b_cigar[pchl] == 'M')
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_up_right < lv_up_left) && (lv_down_right > lv_down_left)) //op_dm_l1[tid][v_cnt_i] == -1
{
if (b_cigar[pchl] == 'M')
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if ((lv_down_right <= lv_down_left) && (lv_up_right >= lv_up_left))
{
if (f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for (f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p2 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_m_n);
snt += sn;
}
#ifdef CIGAR_S_MODIFY
if(lv_down_right < read_length2)
{
sn = sprintf(cigar_p2 + snt, "%uS", read_length2 - lv_down_right);
snt += sn;
}
#else
if (m_n_b)
{
if (cigar_p2[snt - 1] == 'M')
{
for (bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if ((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uM", m_n_b);
snt = bit_char_i + 1 + sn;
}
else if(cigar_p2[snt - 1] == 'S')
{
for(bit_char_i = snt - 2, f_i = 0; bit_char_i > -1; bit_char_i--, f_i++)
{
if((cigar_p2[bit_char_i] > 64) && (cigar_p2[bit_char_i] < 91)) break;
m_n_b += (cigar_p2[bit_char_i] - '0') * carry_ten[f_i];
}
sn = sprintf(cigar_p2 + bit_char_i + 1, "%uS", m_n_b);
snt = bit_char_i + 1 + sn;
}
else
{
sn = sprintf(cigar_p2 + snt, "%uM", m_n_b);
snt += sn;
}
}
#endif
//sprintf(cigar_p2 + snt, "\0");
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
strncpy(cigar_tmp, cigar_p2, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p2[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length2 != cigar_len)
{
if(read_length2 < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length2);
if(cigar_len_re > 0) sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p2 + snt - sn, "\0");
else strcpy(cigar_p2, cigar_m2[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length2 - cigar_len);
sprintf(cigar_p2 + snt - sn, "%u%c", cigar_len_re, cigar_p2[snt - 1]);
}
}
#endif
}
sam_pos1s[tid][xa_i] = (uint32_t )(sam_pos1 + i_n1 - d_n1 + s_offset1);
sam_pos2s[tid][xa_i] = (uint32_t )(sam_pos2 + i_n2 - d_n2 + s_offset2);
strcpy(cigar_p1s[tid][xa_i], cigar_p1);
strcpy(cigar_p2s[tid][xa_i], cigar_p2);
lv_re1s[tid][xa_i] = lv_re1;
lv_re2s[tid][xa_i] = lv_re2;
++xa_i;
}
#ifdef MAPPING_QUALITY
if(mp_flag)
{
if(xa_i)
{
log_tmp = log(vs_cnt);
sam_qual1 = (sam_qual1 - sub_t[tid] - log_tmp) * 3.434;
sam_qual1 = (sam_qual1 > 2 ? sam_qual1 : 2);
#ifdef QUAL_20
sam_qual1 = (sam_qual1 < 20 ? 20 : sam_qual1);
#endif
sam_qual1 = (sam_qual1 > 60 ? 60 : sam_qual1);
sam_qual2 = sam_qual1;
#ifdef MP_DEBUG
printf("2: %d %d\n\n", sam_qual1, sam_qual2);
#endif
}
else
{
sam_qual1 = 60;
sam_qual2 = 60;
}
}
#endif
seqio[seqi].qualc1 = sam_qual1;
seqio[seqi].qualc2 = sam_qual2;
#ifdef PR_SINGLE
//plug-in single positions output
xa_i1 = 0;
xa_i2 = 0;
if(pr_o_f[tid] == 1)
{
for(rc_i = 0; rc_i < 2; rc_i++)
for(rc_ii = 0; rc_ii < 2; rc_ii++)
for(v_cnt_i = 0; v_cnt_i < seedpos_misn[rc_i][rc_ii][tid]; v_cnt_i++)
{
if(seedpos_mis[rc_i][rc_ii][tid][v_cnt_i] == min_mis[tid])
{
x = seedpos[rc_i][rc_ii][tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
if(rc_i == rc_ii)
{
if(xa_i1 < pr_single_outputn)
{
pr_chr_res1[tid][xa_i1] = chr_re;
pr_sam_pos1[tid][xa_i1] = x - chr_end_n[chr_re - 1] + 1;
pr_xa_d1[tid][xa_i1] = pr_dir[rc_ii];
pr_lv_re1[tid][xa_i1] = min_mis[tid];
xa_i1++;
}
}
else
{
if(xa_i2 < pr_single_outputn)
{
pr_chr_res2[tid][xa_i2] = chr_re;
pr_sam_pos2[tid][xa_i2] = x - chr_end_n[chr_re - 1] + 1;
pr_xa_d2[tid][xa_i2] = pr_dir[rc_ii];
pr_lv_re2[tid][xa_i2] = min_mis[tid];
xa_i2++;
}
}
}
}
}
#endif
seqio[seqi].v_cnt = v_cnt_out;
//seqio[seqi].xa_n = xa_i;
seqio[seqi].xa_n_p1 = xa_i;
seqio[seqi].xa_n_p2 = xa_i;
#ifdef FIX_SV
seqio[seqi].xa_n_x1 = 0;
seqio[seqi].xa_n_x2 = 0;
#endif
if(xa_i > 0)
{
memcpy(chr_res_buffer[seqi], chr_res[tid], xa_i << 2);
seqio[seqi].chr_res = chr_res_buffer[seqi];
memcpy(xa_d1s_buffer[seqi], xa_d1s[tid], xa_i);
seqio[seqi].xa_d1s = xa_d1s_buffer[seqi];
memcpy(sam_pos1s_buffer[seqi], sam_pos1s[tid], xa_i << 2);
seqio[seqi].sam_pos1s = sam_pos1s_buffer[seqi];
memcpy(lv_re1s_buffer[seqi], lv_re1s[tid], xa_i << 2);
seqio[seqi].lv_re1s = lv_re1s_buffer[seqi];
for(v_cnt_i = 0; v_cnt_i < xa_i; v_cnt_i++)
{
f_i = strlen(cigar_p1s[tid][v_cnt_i]) + 1;
seqio[seqi].cigar_p1s[v_cnt_i] = (char* )malloc(f_i);
memcpy(seqio[seqi].cigar_p1s[v_cnt_i], cigar_p1s[tid][v_cnt_i], f_i);
f_i = strlen(cigar_p2s[tid][v_cnt_i]) + 1;
seqio[seqi].cigar_p2s[v_cnt_i] = (char* )malloc(f_i);
memcpy(seqio[seqi].cigar_p2s[v_cnt_i], cigar_p2s[tid][v_cnt_i], f_i);
}
}
seqio[seqi].xa_n1 = xa_i1;
#ifdef PR_SINGLE
if(pr_o_f[tid] == 1)
{
if(xa_i1 > 0)
{
memcpy(chr_res1_buffer[seqi], pr_chr_res1[tid], xa_i1);
seqio[seqi].chr_res1 = chr_res1_buffer[seqi];
memcpy(xa_ds1_buffer[seqi], pr_xa_d1[tid], xa_i1);
seqio[seqi].xa_ds1 = xa_ds1_buffer[seqi];
memcpy(sam_poss1_buffer[seqi], pr_sam_pos1[tid], xa_i1 << 2);
seqio[seqi].sam_poss1 = sam_poss1_buffer[seqi];
memcpy(lv_res1_buffer[seqi], pr_lv_re1[tid], xa_i1);
seqio[seqi].lv_res1 = lv_res1_buffer[seqi];
}
}
#endif
if(xa_i > 0)
{
memcpy(xa_d2s_buffer[seqi], xa_d2s[tid], xa_i);
seqio[seqi].xa_d2s = xa_d2s_buffer[seqi];
memcpy(sam_pos2s_buffer[seqi], sam_pos2s[tid], xa_i << 2);
seqio[seqi].sam_pos2s = sam_pos2s_buffer[seqi];
memcpy(lv_re2s_buffer[seqi], lv_re2s[tid], xa_i << 2);
seqio[seqi].lv_re2s = lv_re2s_buffer[seqi];
}
seqio[seqi].xa_n2 = xa_i2;
#ifdef PR_SINGLE
if(pr_o_f[tid] == 1)
{
if(xa_i2 > 0)
{
memcpy(chr_res2_buffer[seqi], pr_chr_res2[tid], xa_i2);
seqio[seqi].chr_res2 = chr_res2_buffer[seqi];
memcpy(xa_ds2_buffer[seqi], pr_xa_d2[tid], xa_i2);
seqio[seqi].xa_ds2 = xa_ds2_buffer[seqi];
memcpy(sam_poss2_buffer[seqi], pr_sam_pos2[tid], xa_i2 << 2);
seqio[seqi].sam_poss2 = sam_poss2_buffer[seqi];
memcpy(lv_res2_buffer[seqi], pr_lv_re2[tid], xa_i2);
seqio[seqi].lv_res2 = lv_res2_buffer[seqi];
}
}
#endif
}
#ifdef PAIR_RANDOM
void Adjust(uint32_t* ls, uint32_t s, uint8_t tid)
{
uint32_t i, t;
t = ((s + seedn[tid]) >> 1);
while(t > 0)
{
if(b[tid][s] > b[tid][ls[t]])
{
i = s;
s = ls[t];
ls[t] = i;
}
t >>= 1;
}
ls[0] = s;
}
void CreateLoserTree(uint32_t* ls, uint8_t tid)
{
int64_t i;
b[tid][seedn[tid]] = MINKEY;
for(i = 0; i < seedn[tid]; ++i)
{
ls[i] = seedn[tid];
}
for(i = seedn[tid] - 1; i >= 0; --i)
{
Adjust(ls, i, tid);
}
}
#ifdef UNPIPATH_OFF_K20
void seed_repetitive_single64(uint64_t* read_bit, uint32_t* pos_n, uint64_t** seedpos, uint8_t tid, uint16_t read_length)
#else
void seed_repetitive_single(uint64_t* read_bit, uint32_t* pos_n, uint32_t** seedpos, uint8_t tid, uint16_t read_length)
#endif
{
uint8_t re_d = 0;
uint8_t b_t_n_r = 0;
uint32_t k_i, q, posk_n;
uint32_t ref_pos_n = 0;
uint32_t uni_offset_s_l = 0;
uint16_t read_off = 0;
uint32_t posn = 0;
uint32_t seed_hash = 0;
uint32_t seed_kmer = 0;
uint32_t pos_r_ir = 0;
uint32_t r_ru = 0;
uint32_t ran_p = 0;
uint64_t kmer_bit = 0;
int64_t seed_id_r = 0;
int64_t seed_binary_r = 0;
float r_r = 0;
#ifdef UNPIPATH_OFF_K20
uint64_t kmer_pos_uni = 0;
#else
uint32_t kmer_pos_uni = 0;
#endif
seedn[tid] = 0;
//off_start[tid] = 0;
seed_l[tid] = pair_ran_intvp;
for(read_off = 0; read_off <= read_length - k_t; read_off += seed_l[tid])
{
//if(read_off + k_t - 1 <= r_b_v) continue;
re_d = (read_off & 0X1f);
b_t_n_r = 32 - re_d;
#ifdef HASH_KMER_READ_J
if(re_d <= re_b)
{
kmer_bit = ((read_bit[read_off >> 5] & bit_tran_re[re_d]) >> ((re_b - re_d) << 1));
}
else
{
kmer_bit = (((read_bit[read_off >> 5] & bit_tran_re[re_d]) << ((re_d - re_b) << 1)) | (read_bit[(read_off >> 5) + 1] >> ((re_2bt - re_d) << 1)));
}
#else
tran_tmp_p = (read_bit[read_off >> 5] & bit_tran_re[re_d]);
//or use this method to deal with: & bit_tran_re[b_t_n_r]
kmer_bit = (((read_bit[(read_off >> 5) + 1] >> (b_t_n_r << 1)) & bit_tran_re[b_t_n_r]) | (tran_tmp_p << (re_d << 1)));
kmer_bit >>= re_bt;
#endif
seed_kmer = (kmer_bit & bit_tran[k_r]);
seed_hash = (kmer_bit >> (k_r << 1));
//find the kmer
#ifdef UNPIPATH_OFF_K20
seed_binary_r = binsearch_offset64(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#else
seed_binary_r = binsearch_offset(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#endif
if(seed_binary_r == -1)
continue;
//binary search on unipath offset to get the unipathID
kmer_pos_uni = buffer_off_g[seed_binary_r];//this kmer's offset on unipath
#ifdef UNPIPATH_OFF_K20
seed_id_r = binsearch_interval_unipath64(kmer_pos_uni, buffer_seqf, result_seqf);
#else
seed_id_r = binsearch_interval_unipath(kmer_pos_uni, buffer_seqf, result_seqf);
#endif
ref_pos_n = buffer_pp[seed_id_r + 1] - buffer_pp[seed_id_r];
uni_offset_s_l = kmer_pos_uni - buffer_seqf[seed_id_r];
if(ref_pos_n > pos_n_max)
{
if(ref_pos_n <= RANDOM_RANGE)
{
for(pos_r_ir = 0; pos_r_ir < ref_pos_n; pos_r_ir++)
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + pos_r_ir] + uni_offset_s_l - read_off;
seed_k_pos[tid][seedn[tid]][pos_r_ir] = MAXKEY;
seedn[tid]++;
}
else
{
#ifdef PAIR_RANDOM_SEED
ran_p = (uint32_t )rand();
r_r = ((float)ref_pos_n / RANDOM_RANGE_MAX);
if(r_r >= 2)
{
r_ru = (uint32_t )r_r;
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE; pos_r_ir++, ran_p++)
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + (pos_r_ir * r_ru) + (random_buffer[ran_p & 0Xfff] % r_ru)] + uni_offset_s_l - read_off;
}
else
{
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE; pos_r_ir++)
{
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + (uint32_t )(seed_r_dup[pos_r_ir] * r_r)] + uni_offset_s_l - read_off;
}
}
seed_k_pos[tid][seedn[tid]][pos_r_ir] = MAXKEY;
seedn[tid]++;
#else
r_r = ((float)ref_pos_n / RANDOM_RANGE);
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE; pos_r_ir++)
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + (uint32_t )(pos_r_ir * r_r)] + uni_offset_s_l - read_off;
seed_k_pos[tid][seedn[tid]][pos_r_ir] = MAXKEY;
seedn[tid]++;
#endif
}
}
}
posk_n = 0;
for(k_i = 0; k_i < seedn[tid]; ++k_i)
{
b[tid][k_i] = seed_k_pos[tid][k_i][kcol[tid][k_i]++];
}
CreateLoserTree(ls[tid], tid);
while(b[tid][ls[tid][0]] != MAXKEY)
{
q = ls[tid][0];
seedposk[tid][posk_n++] = b[tid][q];
if(kcol[tid][q] < MAX_COL)
{
b[tid][q] = seed_k_pos[tid][q][kcol[tid][q]++];
Adjust(ls[tid],q, tid);
}
}
memset(kcol[tid], 0, seedn[tid] << 2);
posn = 1;
(*seedpos)[0] = seedposk[tid][0];
for(k_i = 1; k_i < posk_n; k_i++)
{
if(seedposk[tid][k_i] != seedposk[tid][k_i - 1])
(*seedpos)[posn++] = seedposk[tid][k_i];
}
(*pos_n) = posn;
}
void seed_repetitive(uint8_t tid, uint16_t read_length1, uint16_t read_length2, uint16_t f_cigarn, uint16_t ref_copy_num1, uint16_t ref_copy_num2, uint32_t ref_copy_num_chars1, uint32_t ref_copy_num_chars2, cnt_re* cnt, uint32_t seqi, uint16_t lv_k1, uint16_t lv_k2, int16_t pound_pos1_f_forward, int16_t pound_pos1_f_reverse, int16_t pound_pos1_r_forward, int16_t pound_pos1_r_reverse, int16_t pound_pos2_f_forward, int16_t pound_pos2_f_reverse, int16_t pound_pos2_r_forward, int16_t pound_pos2_r_reverse)
{
uint8_t rc_i = 0;
uint8_t rc_ii = 0;
uint8_t re_d = 0;
uint8_t b_t_n_r = 0;
uint8_t q_n1 = 0;
uint8_t c_m_f = 0;
uint8_t max_mismatch = 0;
uint16_t rst_i = 0;
uint16_t s_m_t = 0;
uint16_t read_b_i = 0;
uint16_t ref_copy_num = 0;
uint16_t end_dis[2];
uint16_t read_length = 0;
int bit_char_i = 0;
int dm1 = 0;
int dmt1 = 0;
int lv_dmt1 = 0;
int dm12 = 0;
int dm_l1 = 0;
int dm_r1 = 0;
int ld1 = 0;
int rd1 = 0;
int ld2 = 0;
int rd2 = 0;
int s_r_o_l1 = 0;
int s_r_o_r1 = 0;
int cmp_re = 0;
int q_rear_i = 0;
int q_rear1 = 0;
int cache_dml1[MAX_Q_NUM];
int cache_dmr1[MAX_Q_NUM];
int cache_dis1[MAX_Q_NUM];
uint32_t ref_copy_num_chars = 0;
uint32_t ref_copy_num_chars_1 = 0;
uint32_t ref_copy_num_chars_2 = 0;
uint32_t pos1_t = 0;
uint32_t pos2_t = 0;
uint32_t seed_nt = 0;
uint32_t seed_nt1 = 0;
uint32_t seed_nt2 = 0;
uint32_t inner_n = 0;
uint32_t seed_sn = 0;
uint32_t seednn[2];
uint32_t mis_c_n = 0;
uint32_t mis_c_n_filt = 0;
int64_t b_r_s = 0;
int64_t b_r_s_i = 0;
uint64_t tran_tmp_p = 0;
uint64_t tran_tmp = 0;
uint64_t xor_tmp = 0;
uint64_t ref_tmp_ori = 0;
uint64_t ref_tmp_ori2 = 0;
uint64_t cache_end1[MAX_Q_NUM][MAX_REF_SEQ_C];
uint64_t low_mask = 0;
uint16_t* sub_mask = NULL;
uint64_t* ex_d_mask = NULL;
dm_op[tid] = MAX_OP_SCORE;
dm_ops[tid] = MAX_OP_SCORE;
cnt->v_cnt = 0;
cnt->vs_cnt = 0;
#ifdef QUAL_FILT_REP
uint64_t* qual_filt_1 = NULL;
#endif
#ifdef PR_SINGLE
min_mis[tid] = 0Xff;
seedpos_misn[0][0][tid] = 0;
seedpos_misn[0][1][tid] = 0;
seedpos_misn[1][0][tid] = 0;
seedpos_misn[1][1][tid] = 0;
#endif
#ifdef UNPIPATH_OFF_K20
uint64_t pos_l = 0;
uint64_t pos_t1 = 0;
uint64_t pos_t2 = 0;
uint64_t posi = 0;
uint64_t up_pos = 0;
uint64_t down_pos = 0;
uint64_t* seed_pt = NULL;
#else
uint32_t pos_l = 0;
uint32_t pos_t1 = 0;
uint32_t pos_t2 = 0;
uint32_t posi = 0;
uint32_t up_pos = 0;
uint32_t down_pos = 0;
uint32_t* seed_pt = NULL;
#endif
end_dis[0] = end_dis1[tid];
end_dis[1] = end_dis2[tid];
for(rc_i = 0; rc_i < 2; rc_i++)
{
//check whether can make pair
if((pos_ren[rc_i][0][tid] == 0) || (pos_ren[rc_i][1][tid] == 0)) continue;
#ifdef UNPIPATH_OFF_K20
seed_repetitive_single64(read_bit1[tid][rc_i], &(seed_posn[rc_i][tid]), &(seedpos[rc_i][rc_i][tid]), tid, read_length1);
seed_repetitive_single64(read_bit2[tid][1 - rc_i], &(seed_posn[1 - rc_i][tid]), &(seedpos[rc_i][1 - rc_i][tid]), tid, read_length2);
#else
seed_repetitive_single(read_bit1[tid][rc_i], &(seed_posn[rc_i][tid]), &(seedpos[rc_i][rc_i][tid]), tid, read_length1);
seed_repetitive_single(read_bit2[tid][1 - rc_i], &(seed_posn[1 - rc_i][tid]), &(seedpos[rc_i][1 - rc_i][tid]), tid, read_length2);
#endif
seed_nt1 = seed_posn[0][tid];
seed_nt2 = seed_posn[1][tid];
if((seed_nt1 == 0) || (seed_nt2 == 0)) continue;
#ifdef PR_SINGLE
//do exact match to get mismatch number on every position in seedpos
for(rc_ii = 0; rc_ii < 2; rc_ii++)
{
if(rc_i == rc_ii)
{
ref_copy_num_chars = ref_copy_num_chars1;
ref_copy_num = ref_copy_num1;
low_mask = low_mask1[tid];
sub_mask = sub_mask1[tid];
ex_d_mask = ex_d_mask1[tid];
max_mismatch = max_mismatch1[tid];
#ifdef QUAL_FILT_REP
if(rc_i == 0) qual_filt_1 = qual_filt1[tid][0];
else qual_filt_1 = qual_filt1[tid][1];
#endif
}
else
{
ref_copy_num_chars = ref_copy_num_chars2;
ref_copy_num = ref_copy_num2;
low_mask = low_mask2[tid];
sub_mask = sub_mask2[tid];
ex_d_mask = ex_d_mask2[tid];
max_mismatch = max_mismatch2[tid];
#ifdef QUAL_FILT_REP
if(rc_i == 0) qual_filt_1 = qual_filt2[tid][1];
else qual_filt_1 = qual_filt2[tid][0];
#endif
}
read_bit_1[tid] = read_bit_pr[tid][(rc_i << 1) + rc_ii];
for(pos1_t = 0; pos1_t < seed_posn[rc_ii][tid]; pos1_t++)
{
pos_l = seedpos[rc_i][rc_ii][tid][pos1_t] - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars);
for(rst_i = 0; rst_i < ref_copy_num - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask;
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num - 1] &= low_mask;
}
//trim the beginning and end of the current ref seq based on current minimum edit distance dm_t
s_m_t = sub_mask[0];
ref_seq_tmp1[tid][0] &= bit_tran[0];
ref_seq_tmp1[tid][s_m_t] &= ex_d_mask[0];
mis_c_n = 0;
#ifdef QUAL_FILT_REP
mis_c_n_filt = 0;
#endif
//ref_tmp_ori = ref_seq_tmp1[ref_copy_num - 2];
ref_seq_tmp1[tid][ref_copy_num - 2] &= low_mask;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT_REP
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch) break;
#endif
}
if(mis_c_n_filt > max_mismatch)
{
seedpos_mis[rc_i][rc_ii][tid][pos1_t] = MAX_SPM;
}
else
{
seedpos_mis[rc_i][rc_ii][tid][pos1_t] = mis_c_n;
if(mis_c_n < min_mis[tid]) min_mis[tid] = mis_c_n;
}
}
seedpos_misn[rc_i][rc_ii][tid] = seed_posn[rc_ii][tid];
}
#endif
memset(seed_posf[0][tid], 0, seed_nt1);
memset(seed_posf[1][tid], 0, seed_nt2);
for(pos1_t = 0, pos2_t = 0; (pos1_t < seed_nt1) && (pos2_t < seed_nt2); pos1_t++)
{
up_pos = seedpos[rc_i][0][tid][pos1_t] + end_dis[rc_i] - devi;
down_pos = seedpos[rc_i][0][tid][pos1_t] + end_dis[rc_i] + devi;
seed_pt = seedpos[rc_i][1][tid];
inner_n = 0;
for( ; (seed_pt[pos2_t] < down_pos) && (pos2_t < seed_nt2); pos2_t++)
if(seed_pt[pos2_t] > up_pos)
{
seed_posf[1][tid][pos2_t] = 1;
inner_n++;
}
if(inner_n > 0) seed_posf[0][tid][pos1_t] = 1;
}
for(pos1_t = 0, pos2_t = 0; (pos1_t < seed_nt1) && (pos2_t < seed_nt2); pos2_t++)
{
up_pos = seedpos[rc_i][1][tid][pos2_t] - end_dis[rc_i] - devi;
down_pos = seedpos[rc_i][1][tid][pos2_t] - end_dis[rc_i] + devi;
seed_pt = seedpos[rc_i][0][tid];
inner_n = 0;
for( ; (seed_pt[pos1_t] < down_pos) && (pos1_t < seed_nt2); pos1_t++)
if(seed_pt[pos1_t] > up_pos)
{
seed_posf[0][tid][pos1_t] = 1;
inner_n++;
}
if(inner_n > 0) seed_posf[1][tid][pos2_t] = 1;
}
for(rc_ii = 0; rc_ii < 2; rc_ii++)
{
if(rc_i == rc_ii)
{
ref_copy_num_chars = ref_copy_num_chars1;
ref_copy_num = ref_copy_num1;
low_mask = low_mask1[tid];
sub_mask = sub_mask1[tid];
ex_d_mask = ex_d_mask1[tid];
lv_dmt1 = lv_k1;
read_length = read_length1;
max_mismatch = max_mismatch1[tid];
#ifdef QUAL_FILT_REP
if(rc_i == 0) qual_filt_1 = qual_filt1[tid][0];
else qual_filt_1 = qual_filt1[tid][1];
#endif
}
else
{
ref_copy_num_chars = ref_copy_num_chars2;
ref_copy_num = ref_copy_num2;
low_mask = low_mask2[tid];
sub_mask = sub_mask2[tid];
ex_d_mask = ex_d_mask2[tid];
lv_dmt1 = lv_k2;
read_length = read_length2;
max_mismatch = max_mismatch2[tid];
#ifdef QUAL_FILT_REP
if(rc_i == 0) qual_filt_1 = qual_filt2[tid][1];
else qual_filt_1 = qual_filt2[tid][0];
#endif
}
read_bit_1[tid] = read_bit_pr[tid][(rc_i << 1) + rc_ii];
read_val_1[tid] = read_val_pr[tid][(rc_i << 1) + rc_ii];
q_rear1 = 0;
q_n1 = 0;
dmt1 = ali_exl;
s_r_o_l1 = 0;
s_r_o_r1 = 0;
seed_sn = 0;
for(pos1_t = 0; pos1_t < seed_posn[rc_ii][tid]; pos1_t++)
{
if(seed_posf[rc_ii][tid][pos1_t] == 1)
{
#ifdef PR_SINGLE
if(seedpos_mis[rc_i][rc_ii][tid][pos1_t] == MAX_SPM)
{
#endif
//lv_f1 = 0;
pos_l = seedpos[rc_i][rc_ii][tid][pos1_t] - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars);
for(rst_i = 0; rst_i < ref_copy_num - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask;
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num - 1] &= low_mask;
}
//trim the beginning and end of the current ref seq based on current minimum edit distance dm_t
s_m_t = sub_mask[dmt1];
ref_seq_tmp1[tid][0] &= bit_tran[dmt1];
ref_seq_tmp1[tid][s_m_t] &= ex_d_mask[dmt1];
//traverse and check whether there is an existing seq that is as same as current new ref seq
c_m_f = 0;
for(q_rear_i = q_rear1 - 1; q_rear_i >= 0; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask[dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
c_m_f = 1;
break;
}
}
if((q_n1 > MAX_Q_NUM) && (q_rear_i < 0))
{
for(q_rear_i = MAX_Q_NUM - 1; q_rear_i >= q_rear1; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask[dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
c_m_f = 1;
break;
}
}
}
//do not find the seq in cache, exact match or lv and add into cache
if(c_m_f == 0)
{
#ifdef PR_SINGLE
mis_c_n = max_mismatch + 1;
#else
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT_REP
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num - 2];
ref_seq_tmp1[tid][ref_copy_num - 2] &= low_mask;
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT_REP
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch) break;
#endif
}
ref_seq_tmp1[tid][ref_copy_num - 2] = ref_tmp_ori;
#endif
//lv
if(mis_c_n_filt > max_mismatch)
{
#ifdef SPLIT_LV
//split lv
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - bit_char_i) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - bit_char_i) << 1)) & 0X3);
#ifdef LV_CIGAR
dm_l1 = computeEditDistanceWithCigar(ali_ref_seq[tid], 33 + s_r_o_l1, read_char[tid], s_r_o_l1 + 1, dmt1, cigarBuf, f_cigarn, 0, 0, L[tid]);
#else
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + s_r_o_l1, read_char[tid], s_r_o_l1 + 1, lv_dmt1, L[tid]);
#endif
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - bit_char_i) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - bit_char_i) << 1)) & 0X3);
#ifdef LV_CIGAR
dm_r1 = computeEditDistanceWithCigar(ali_ref_seq[tid], 32 + read_length - s_r_o_r1, read_char[tid], read_length - s_r_o_r1, dmt1, cigarBuf, f_cigarn, 0, 0, L[tid]);
#else
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + read_length - s_r_o_r1, read_char[tid], read_length - s_r_o_r1, lv_dmt1, L[tid]);
#endif
dm1 = dm_l1 + dm_r1;
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
dm1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1))
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch - 1) dmt1 = 0;
}
else dm1 = MAX_EDIT_SCORE;
//add the ref sequence at the end of queue
memcpy(cache_end1[q_rear1], ref_seq_tmp1[tid], ref_copy_num_chars);
cache_dis1[q_rear1] = dm1;
cache_dml1[q_rear1] = ld1;
cache_dmr1[q_rear1] = rd1;
q_rear1 = ((q_rear1 + 1) & 0X1f);
++q_n1;
//add edit distance
}
if(dm1 != MAX_EDIT_SCORE)
{
seed_single_pos[rc_ii][tid][seed_sn] = seedpos[rc_i][rc_ii][tid][pos1_t];
seed_single_ld[rc_ii][tid][seed_sn] = ld1;
seed_single_rd[rc_ii][tid][seed_sn] = rd1;
seed_single_dm[rc_ii][tid][seed_sn] = dm1;
memcpy(seed_single_refs[rc_ii][tid][seed_sn], ref_seq_tmp1[tid], ref_copy_num_chars);
seed_sn++;
}
#ifdef PR_SINGLE
}
else
{
seed_single_pos[rc_ii][tid][seed_sn] = seedpos[rc_i][rc_ii][tid][pos1_t];
seed_single_ld[rc_ii][tid][seed_sn] = 0;
seed_single_rd[rc_ii][tid][seed_sn] = 0;
seed_single_dm[rc_ii][tid][seed_sn] = seedpos_mis[rc_i][rc_ii][tid][pos1_t];
seed_sn++;
}
#endif
}
}
seednn[rc_ii] = seed_sn;
}
if((seednn[0] == 0) || (seednn[1] == 0)) continue;
if(rc_i == 0)
{
ref_copy_num_chars_1 = ref_copy_num_chars1;
ref_copy_num_chars_2 = ref_copy_num_chars2;
}
else
{
ref_copy_num_chars_1 = ref_copy_num_chars2;
ref_copy_num_chars_2 = ref_copy_num_chars1;
}
if(seednn[0] <= seednn[1])
{
for(pos1_t = 0; pos1_t < seednn[0]; pos1_t++)
{
pos_t1 = seed_single_pos[0][tid][pos1_t];
posi = pos_t1 + end_dis[rc_i];
#ifdef UNPIPATH_OFF_K20
b_r_s = binsearch_seed_pos_ss64(posi, seed_single_pos[1][tid], seednn[1]);
#else
b_r_s = binsearch_seed_pos_ss(posi, seed_single_pos[1][tid], seednn[1]);
#endif
if(b_r_s != -1)
{
dm12 = seed_single_dm[0][tid][pos1_t] + seed_single_dm[1][tid][b_r_s];
pos_t2 = seed_single_pos[1][tid][b_r_s];
ld1 = seed_single_ld[0][tid][pos1_t];
ld2 = seed_single_ld[1][tid][b_r_s];
rd1 = seed_single_rd[0][tid][pos1_t];
rd2 = seed_single_rd[1][tid][b_r_s];
memcpy(ref_seq_tmp1[tid], seed_single_refs[0][tid][pos1_t], ref_copy_num_chars_1);
memcpy(ref_seq_tmp2[tid], seed_single_refs[1][tid][b_r_s], ref_copy_num_chars_2);
#ifdef UNPIPATH_OFF_K20
cnt = pair_op_add64(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][pos1_t], seed_single_dm[1][tid][b_r_s], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#else
cnt = pair_op_add(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][pos1_t], seed_single_dm[1][tid][b_r_s], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#endif
#ifdef PAIR_TRAVERSE
for(b_r_s_i = b_r_s + 1; (seed_single_pos[1][tid][b_r_s_i] < posi + devi) && (b_r_s_i < seednn[1]); b_r_s_i++)
{
dm12 = seed_single_dm[0][tid][pos1_t] + seed_single_dm[1][tid][b_r_s_i];
pos_t2 = seed_single_pos[1][tid][b_r_s_i];
ld2 = seed_single_ld[1][tid][b_r_s_i];
rd2 = seed_single_rd[1][tid][b_r_s_i];
memcpy(ref_seq_tmp2[tid], seed_single_refs[1][tid][b_r_s_i], ref_copy_num_chars_2);
#ifdef UNPIPATH_OFF_K20
cnt = pair_op_add64(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][pos1_t], seed_single_dm[1][tid][b_r_s_i], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#else
cnt = pair_op_add(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][pos1_t], seed_single_dm[1][tid][b_r_s_i], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#endif
}
for(b_r_s_i = b_r_s - 1; (seed_single_pos[1][tid][b_r_s_i] > posi - devi) && (b_r_s_i >= 0); b_r_s_i--)
{
dm12 = seed_single_dm[0][tid][pos1_t] + seed_single_dm[1][tid][b_r_s_i];
pos_t2 = seed_single_pos[1][tid][b_r_s_i];
ld2 = seed_single_ld[1][tid][b_r_s_i];
rd2 = seed_single_rd[1][tid][b_r_s_i];
memcpy(ref_seq_tmp2[tid], seed_single_refs[1][tid][b_r_s_i], ref_copy_num_chars_2);
#ifdef UNPIPATH_OFF_K20
cnt = pair_op_add64(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][pos1_t], seed_single_dm[1][tid][b_r_s_i], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#else
cnt = pair_op_add(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][pos1_t], seed_single_dm[1][tid][b_r_s_i], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#endif
}
#endif
}
}
}
else
{
for(pos2_t = 0; pos2_t < seednn[1]; pos2_t++)
{
pos_t2 = seed_single_pos[1][tid][pos2_t];
posi = pos_t2 - end_dis[rc_i];
#ifdef UNPIPATH_OFF_K20
b_r_s = binsearch_seed_pos_ss64(posi, seed_single_pos[0][tid], seednn[0]);
#else
b_r_s = binsearch_seed_pos_ss(posi, seed_single_pos[0][tid], seednn[0]);
#endif
if(b_r_s != -1)
{
dm12 = seed_single_dm[1][tid][pos2_t] + seed_single_dm[0][tid][b_r_s];
pos_t1 = seed_single_pos[0][tid][b_r_s];
ld1 = seed_single_ld[0][tid][b_r_s];
ld2 = seed_single_ld[1][tid][pos2_t];
rd1 = seed_single_rd[0][tid][b_r_s];
rd2 = seed_single_rd[1][tid][pos2_t];
memcpy(ref_seq_tmp1[tid], seed_single_refs[0][tid][b_r_s], ref_copy_num_chars_1);
memcpy(ref_seq_tmp2[tid], seed_single_refs[1][tid][pos2_t], ref_copy_num_chars_2);
#ifdef UNPIPATH_OFF_K20
cnt = pair_op_add64(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][b_r_s], seed_single_dm[1][tid][pos2_t],tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#else
cnt = pair_op_add(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][b_r_s], seed_single_dm[1][tid][pos2_t],tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#endif
#ifdef PAIR_TRAVERSE
for(b_r_s_i = b_r_s + 1; (seed_single_pos[0][tid][b_r_s_i] < posi + devi) && (b_r_s_i < seednn[0]); b_r_s_i++)
{
dm12 = seed_single_dm[1][tid][pos2_t] + seed_single_dm[0][tid][b_r_s_i];
pos_t1 = seed_single_pos[0][tid][b_r_s_i];
ld1 = seed_single_ld[0][tid][b_r_s_i];
rd1 = seed_single_rd[0][tid][b_r_s_i];
memcpy(ref_seq_tmp1[tid], seed_single_refs[0][tid][b_r_s_i], ref_copy_num_chars_1);
#ifdef UNPIPATH_OFF_K20
cnt = pair_op_add64(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][b_r_s_i], seed_single_dm[1][tid][pos2_t], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#else
cnt = pair_op_add(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][b_r_s_i], seed_single_dm[1][tid][pos2_t], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#endif
}
for(b_r_s_i = b_r_s - 1; (seed_single_pos[0][tid][b_r_s_i] > posi - devi) && (b_r_s_i >= 0); b_r_s_i--)
{
dm12 = seed_single_dm[1][tid][pos2_t] + seed_single_dm[0][tid][b_r_s_i];
pos_t1 = seed_single_pos[0][tid][b_r_s_i];
ld1 = seed_single_ld[0][tid][b_r_s_i];
rd1 = seed_single_rd[0][tid][b_r_s_i];
memcpy(ref_seq_tmp1[tid], seed_single_refs[0][tid][b_r_s_i], ref_copy_num_chars_1);
#ifdef UNPIPATH_OFF_K20
cnt = pair_op_add64(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][b_r_s_i], seed_single_dm[1][tid][pos2_t], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#else
cnt = pair_op_add(pos_t1, pos_t2, ld1, rd1, ld2, rd2, dm12, rc_i, seed_single_dm[0][tid][b_r_s_i], seed_single_dm[1][tid][pos2_t], tid, ref_copy_num_chars1, ref_copy_num_chars2, cnt);
#endif
}
#endif
}
}
}
}
if(cnt->v_cnt > 0)
{
de_m_p_o[tid] = 0;
#ifdef ALI_OUT
#ifdef PR_SINGLE
pr_o_f[tid] = 1;
#endif
pair_sam_output(tid, read_length1, read_length2, f_cigarn, cnt, seqi, lv_k1, lv_k2, pound_pos1_f_forward, pound_pos1_f_reverse, pound_pos1_r_forward, pound_pos1_r_reverse, pound_pos2_f_forward, pound_pos2_f_reverse, pound_pos2_r_forward, pound_pos2_r_reverse, cir_fix_n - 1);
#endif
}
}
#ifdef UNPIPATH_OFF_K20
cnt_re* pair_op_add64(uint64_t pos_t1, uint64_t pos_t2, int ld1, int rd1, int ld2, int rd2, int dm12, uint8_t rc_i, int dm1, int dm2, uint8_t tid, uint32_t ref_copy_num_chars1, uint32_t ref_copy_num_chars2, cnt_re* cnt)
#else
cnt_re* pair_op_add(uint32_t pos_t1, uint32_t pos_t2, int ld1, int rd1, int ld2, int rd2, int dm12, uint8_t rc_i, int dm1, int dm2, uint8_t tid, uint32_t ref_copy_num_chars1, uint32_t ref_copy_num_chars2, cnt_re* cnt)
#endif
{
uint16_t dm_i = 0;
uint32_t v_cnt = 0;
uint32_t vs_cnt = 0;
v_cnt = cnt->v_cnt;
vs_cnt = cnt->vs_cnt;
if(dm12 < dm_op[tid])
{
#ifdef DM_COPY_REP
for(dm_i = 0; dm_i < v_cnt; dm_i++)
{
ops_vector_pos1[tid][dm_i] = op_vector_pos1[tid][dm_i];
ops_dm_l1[tid][dm_i] = op_dm_l1[tid][dm_i];
ops_dm_r1[tid][dm_i] = op_dm_r1[tid][dm_i];
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars1);
#else
if(!((op_dm_l1[tid][dm_i] == 0) && (op_dm_r1[tid][dm_i] == 0)))
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars1);
#endif
ops_dm_ex1[tid][dm_i] = op_dm_ex1[tid][dm_i];
ops_vector_pos2[tid][dm_i] = op_vector_pos2[tid][dm_i];
ops_dm_l2[tid][dm_i] = op_dm_l2[tid][dm_i];
ops_dm_r2[tid][dm_i] = op_dm_r2[tid][dm_i];
if(!((op_dm_l2[tid][dm_i] == 0) && (op_dm_r2[tid][dm_i] == 0)))
memcpy(ops_vector_seq2[tid][dm_i], op_vector_seq2[tid][dm_i], ref_copy_num_chars2);
ops_dm_ex2[tid][dm_i] = op_dm_ex2[tid][dm_i];
}
vs_cnt = v_cnt;
dm_ops[tid] = dm_op[tid];
#endif
v_cnt = 0;
if(rc_i == 0)
{
op_vector_pos1[tid][v_cnt] = pos_t1;
op_vector_pos2[tid][v_cnt] = pos_t2;
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
op_dm_l2[tid][v_cnt] = ld2;
op_dm_r2[tid][v_cnt] = rd2;
op_dm_ex1[tid][v_cnt] = dm1;
op_dm_ex2[tid][v_cnt] = dm2;
}
else
{
op_vector_pos1[tid][v_cnt] = pos_t2;
op_vector_pos2[tid][v_cnt] = pos_t1;
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld2;
op_dm_r1[tid][v_cnt] = rd2;
op_dm_l2[tid][v_cnt] = ld1;
op_dm_r2[tid][v_cnt] = rd1;
op_dm_ex1[tid][v_cnt] = dm2;
op_dm_ex2[tid][v_cnt] = dm1;
}
op_rc[tid][v_cnt] = rc_i;
++v_cnt;
dm_op[tid] = dm12;
}
else if(dm12 == dm_op[tid])
{
if(v_cnt < cus_max_output_ali)
{
if(rc_i == 0)
{
op_vector_pos1[tid][v_cnt] = pos_t1;
op_vector_pos2[tid][v_cnt] = pos_t2;
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
op_dm_l2[tid][v_cnt] = ld2;
op_dm_r2[tid][v_cnt] = rd2;
op_dm_ex1[tid][v_cnt] = dm1;
op_dm_ex2[tid][v_cnt] = dm2;
}
else
{
op_vector_pos1[tid][v_cnt] = pos_t2;
op_vector_pos2[tid][v_cnt] = pos_t1;
#ifdef MAPPING_QUALITY
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq2[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
op_dm_l1[tid][v_cnt] = ld2;
op_dm_r1[tid][v_cnt] = rd2;
op_dm_l2[tid][v_cnt] = ld1;
op_dm_r2[tid][v_cnt] = rd1;
op_dm_ex1[tid][v_cnt] = dm2;
op_dm_ex2[tid][v_cnt] = dm1;
}
op_rc[tid][v_cnt] = rc_i;
++v_cnt;
}
}
else if(dm12 < dm_ops[tid])
{
vs_cnt = 0;
if(rc_i == 0)
{
ops_vector_pos1[tid][vs_cnt] = pos_t1;
ops_vector_pos2[tid][vs_cnt] = pos_t2;
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
ops_dm_l2[tid][vs_cnt] = ld2;
ops_dm_r2[tid][vs_cnt] = rd2;
ops_dm_ex1[tid][vs_cnt] = dm1;
ops_dm_ex2[tid][vs_cnt] = dm2;
}
else
{
ops_vector_pos1[tid][vs_cnt] = pos_t2;
ops_vector_pos2[tid][vs_cnt] = pos_t1;
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld2;
ops_dm_r1[tid][vs_cnt] = rd2;
ops_dm_l2[tid][vs_cnt] = ld1;
ops_dm_r2[tid][vs_cnt] = rd1;
ops_dm_ex1[tid][vs_cnt] = dm2;
ops_dm_ex2[tid][vs_cnt] = dm1;
}
ops_rc[tid][vs_cnt] = rc_i;
++vs_cnt;
dm_ops[tid] = dm12;
}
else if(dm12 == dm_ops[tid])
{
if(vs_cnt < cus_max_output_ali)
{
if(rc_i == 0)
{
ops_vector_pos1[tid][vs_cnt] = pos_t1;
ops_vector_pos2[tid][vs_cnt] = pos_t2;
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars1);
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
ops_dm_l2[tid][vs_cnt] = ld2;
ops_dm_r2[tid][vs_cnt] = rd2;
ops_dm_ex1[tid][vs_cnt] = dm1;
ops_dm_ex2[tid][vs_cnt] = dm2;
}
else
{
ops_vector_pos1[tid][vs_cnt] = pos_t2;
ops_vector_pos2[tid][vs_cnt] = pos_t1;
#ifdef MAPPING_QUALITY
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#else
if(!((ld2 == 0) && (rd2 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp2[tid], ref_copy_num_chars1);
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq2[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars2);
#endif
ops_dm_l1[tid][vs_cnt] = ld2;
ops_dm_r1[tid][vs_cnt] = rd2;
ops_dm_l2[tid][vs_cnt] = ld1;
ops_dm_r2[tid][vs_cnt] = rd1;
ops_dm_ex1[tid][vs_cnt] = dm2;
ops_dm_ex2[tid][vs_cnt] = dm1;
}
ops_rc[tid][vs_cnt] = rc_i;
++vs_cnt;
}
}
cnt->v_cnt = v_cnt;
cnt->vs_cnt = vs_cnt;
return cnt;
}
void seed_repetitive_single_end(uint64_t* read_bit, uint8_t tid, uint16_t read_length)
{
uint8_t re_d = 0;
uint8_t b_t_n_r = 0;
uint32_t ref_pos_n = 0;
uint32_t uni_offset_s_l = 0;
uint32_t uni_offset_s_r = 0;
uint16_t read_off = 0;
uint16_t left_i = 1;
uint16_t right_i = 1;
uint16_t r_b_v = 0;
uint32_t seed_hash = 0;
uint32_t seed_kmer = 0;
uint32_t pos_r_ir = 0;
uint32_t r_ru = 0;
uint32_t ran_p = 0;
uint64_t kmer_bit = 0;
int64_t seed_id_r = 0;
int64_t seed_binary_r = 0;
float r_r = 0;
#ifdef UNPIPATH_OFF_K20
uint64_t kmer_pos_uni = 0;
#else
uint32_t kmer_pos_uni = 0;
#endif
r_b_v = 0;
seedn[tid] = 0;
seed_l[tid] = pair_ran_intvp;
for(read_off = 0; read_off <= read_length - k_t; read_off += seed_l[tid])
{
if(read_off + k_t - 1 <= r_b_v) continue;
re_d = (read_off & 0X1f);
b_t_n_r = 32 - re_d;
#ifdef HASH_KMER_READ_J
if(re_d <= re_b)
{
kmer_bit = ((read_bit[read_off >> 5] & bit_tran_re[re_d]) >> ((re_b - re_d) << 1));
}
else
{
kmer_bit = (((read_bit[read_off >> 5] & bit_tran_re[re_d]) << ((re_d - re_b) << 1)) | (read_bit[(read_off >> 5) + 1] >> ((re_2bt - re_d) << 1)));
}
#else
tran_tmp_p = (read_bit[read_off >> 5] & bit_tran_re[re_d]);
//or use this method to deal with: & bit_tran_re[b_t_n_r]
kmer_bit = (((read_bit[(read_off >> 5) + 1] >> (b_t_n_r << 1)) & bit_tran_re[b_t_n_r]) | (tran_tmp_p << (re_d << 1)));
kmer_bit >>= re_bt;
#endif
seed_kmer = (kmer_bit & bit_tran[k_r]);
seed_hash = (kmer_bit >> (k_r << 1));
//find the kmer
#ifdef UNPIPATH_OFF_K20
seed_binary_r = binsearch_offset64(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#else
seed_binary_r = binsearch_offset(seed_kmer, buffer_kmer_g, buffer_hash_g[seed_hash + 1] - buffer_hash_g[seed_hash], buffer_hash_g[seed_hash]);
#endif
if(seed_binary_r == -1)
continue;
//binary search on unipath offset to get the unipathID
kmer_pos_uni = buffer_off_g[seed_binary_r];//this kmer's offset on unipath
#ifdef UNPIPATH_OFF_K20
seed_id_r = binsearch_interval_unipath64(kmer_pos_uni, buffer_seqf, result_seqf);
#else
seed_id_r = binsearch_interval_unipath(kmer_pos_uni, buffer_seqf, result_seqf);
#endif
ref_pos_n = buffer_pp[seed_id_r + 1] - buffer_pp[seed_id_r];
uni_offset_s_l = kmer_pos_uni - buffer_seqf[seed_id_r];
uni_offset_s_r = buffer_seqf[seed_id_r + 1] - (kmer_pos_uni + k_t);
if(ref_pos_n > pos_n_max)
{
if(ref_pos_n <= RANDOM_RANGE)
{
for(pos_r_ir = 0; pos_r_ir < ref_pos_n; pos_r_ir++)
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + pos_r_ir] + uni_offset_s_l - read_off;
seed_k_pos[tid][seedn[tid]][pos_r_ir] = MAXKEY;
++seedn[tid];
}
else
{
#ifdef PAIR_RANDOM_SEED
ran_p = (uint32_t )rand();
r_r = ((float)ref_pos_n / RANDOM_RANGE_MAX);
if(r_r >= 2)
{
r_ru = (uint32_t )r_r;
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE; pos_r_ir++, ran_p++)
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + (pos_r_ir * r_ru) + (random_buffer[ran_p & 0Xfff] % r_ru)] + uni_offset_s_l - read_off;
}
else
{
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE; pos_r_ir++)
{
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + (uint32_t )(seed_r_dup[pos_r_ir] * r_r)] + uni_offset_s_l - read_off;
}
}
seed_k_pos[tid][seedn[tid]][pos_r_ir] = MAXKEY;
++seedn[tid];
#else
r_r = ((float)ref_pos_n / RANDOM_RANGE);
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE; pos_r_ir++)
seed_k_pos[tid][seedn[tid]][pos_r_ir] = buffer_p[buffer_pp[seed_id_r] + (uint32_t )(pos_r_ir * r_r)] + uni_offset_s_l - read_off;
seed_k_pos[tid][seedn[tid]][pos_r_ir] = MAXKEY;
++seedn[tid];
#endif
}
for(left_i = 1; (left_i <= uni_offset_s_l) && (left_i <= read_off); left_i++)
{
#ifdef UNI_SEQ64
if(((buffer_seq[(kmer_pos_uni - left_i) >> 5] >> ((31 - ((kmer_pos_uni - left_i) & 0X1f)) << 1)) & 0X3)
!= ((read_bit[(read_off - left_i) >> 5] >> ((31 - ((read_off - left_i) & 0X1f)) << 1)) & 0X3)
) break;
#else
if(((buffer_seq[(kmer_pos_uni - left_i) >> 2] >> (((kmer_pos_uni - left_i) & 0X3) << 1)) & 0X3)
!= ((read_bit[(read_off - left_i) >> 5] >> ((31 - ((read_off - left_i) & 0X1f)) << 1)) & 0X3)
) break;
#endif
}
for(right_i = 1; (right_i <= uni_offset_s_r) && (right_i <= read_length - read_off - k_t); right_i++)
{
#ifdef UNI_SEQ64
if(((buffer_seq[(kmer_pos_uni + k_t - 1 + right_i) >> 5] >> ((31 - ((kmer_pos_uni + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
!= ((read_bit[(read_off + k_t - 1 + right_i) >> 5] >> ((31 - ((read_off + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
) break;
#else
if(((buffer_seq[(kmer_pos_uni + k_t - 1 + right_i) >> 2] >> (((kmer_pos_uni + k_t - 1 + right_i) & 0X3) << 1)) & 0X3)
!= ((read_bit[(read_off + k_t - 1 + right_i) >> 5] >> ((31 - ((read_off + k_t - 1 + right_i) & 0X1f)) << 1)) & 0X3)
) break;
#endif
}
left_dis[tid][seedn[tid] - 1] = read_off - left_i;
right_dis[tid][seedn[tid] - 1] = read_off + k_t + right_i - 1;
r_b_v = read_off + k_t + right_i - 1;
}
}
}
#endif
int seed_ali_single_end(int argc, char *argv[])
{
fprintf(stderr, "single end reads mapping\n\n");
double t = 0.00;
clock_t start = 0, end = 0;
uint16_t v_cnt_i = 0;
uint32_t r_i = 0;
uint32_t seqi = 0;
uint32_t seqii = 0;
int64_t kr1 = 0;
int32_t m = 0;
uint16_t read_length_tmp = 0;
#ifdef PAIR_RANDOM_SEED
uint32_t r_dup_i = 0;
int pos_r_nr = 0;
uint32_t pos_r_ir = 0;
#endif
char h_chars[6];
uint32_t read_in = 0X10000;
uint8_t readlen_name = 255;
start = clock();
load_index_file();
end = clock();
t = (double)(end - start) / CLOCKS_PER_SEC;
seed_l_max = seed_step * cir_fix_n;
fprintf(stderr, "%lf seconds is used for loading index\n", t);
fp1 = gzopen(read_fastq1, "r");
seq1 = kseq_init(fp1);
if(fp1 == NULL)
{
fprintf(stderr, "wrong input file route or name: %s\n", read_fastq1);
exit(1);
}
if(flag_std == 0)
{
fp_sam = fopen(sam_result, "w");
if(fp_sam == NULL)
{
fprintf(stderr, "wrong output file route or name: %s\n", sam_result);
exit(1);
}
}
k_r = k_t - k;
re_b = 32 - k_t;
re_bt = (re_b << 1);
re_2bt = 64 - k_t;
fprintf(stderr, "number of threads running: %u\nmax read length: %u\nseed positions filter: %u\nthe filter number of seed positions: %u\nthe minimum seed interval: %u\nthe number of seed circulation: %u\n", thread_n, readlen_max, pos_n_max, seed_filter_pos_num_singlen, seed_step, cir_fix_n);
pair_ran_intvp = seed_l_max;
#ifdef SEED_FILTER_POS
seed_filter_pos_num_single = seed_filter_pos_num_singlen >> 1;
#endif
//should allocate at beginning
seed_num = ((readlen_max - k_t) / seed_l_l) + 1;
new_seed_cnt = seed_num * pos_n_max;
uint16_t cigar_max_n = MAX_LV_CIGARCOM;
start = clock();
#ifdef PTHREAD_USE
g_low = (int64_t* )calloc(thread_n, 8);
r_low = (int64_t* )calloc(thread_n, 8);
seedm = (seed_m** )calloc(thread_n, sizeof(seed_m* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedm[r_i] = (seed_m* )calloc(seed_num, sizeof(seed_m));
seedu = (seed_m** )calloc(thread_n, sizeof(seed_m* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedu[r_i] = (seed_m* )calloc(seed_num, sizeof(seed_m));
seedsets = (seed_sets** )calloc(thread_n, sizeof(seed_sets* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedsets[r_i] = (seed_sets* )calloc(new_seed_cnt, sizeof(seed_sets));
seed_set_off = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_off[r_i] = (uint32_t* )calloc(new_seed_cnt, sizeof(uint32_t ));
#ifdef SINGLE_PAIR
cov_num_front_single = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
cov_num_re_single = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
#endif
#ifdef UNPIPATH_OFF_K20
seed_set_pos_single = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos_single[r_i] = (uint64_t* )calloc(new_seed_cnt << 1, 8);
#else
seed_set_pos_single = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos_single[r_i] = (uint32_t* )calloc(new_seed_cnt << 1, 4);
#endif
set_pos_n_single = (uint32_t* )calloc(thread_n, 4);
spa_i_single = (uint32_t* )calloc(thread_n, 4);
seedpa1_single = (seed_pa_single** )calloc(thread_n, sizeof(seed_pa_single* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa1_single[r_i] = (seed_pa_single* )calloc(new_seed_cnt << 1, sizeof(seed_pa_single ));
pos_add = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pos_add[r_i] = (uint8_t* )calloc(pos_n_max, 1);
fprintf(stderr, "Load seed reduction allocation\n");
#ifdef UNPIPATH_OFF_K20
op_vector_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos1[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
ops_vector_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos1[r_i] = (uint64_t* )calloc(cus_max_output_ali, 4);
#else
op_vector_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos1[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
ops_vector_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos1[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
#endif
op_dm_l1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_l1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_r1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_r1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_l1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_l1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_r1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_r1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_vector_seq1 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
op_vector_seq1[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((op_vector_seq1[r_i][m] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8)) == NULL)
exit(1);
}
ops_vector_seq1 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
ops_vector_seq1[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((ops_vector_seq1[r_i][m] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8)) == NULL)
exit(1);
}
fprintf(stderr, "Load alignment allocation\n");
#ifdef ALT_ALL
chr_res = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
chr_res[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
sam_pos1s = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
if((sam_pos1s[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(uint32_t ))) == NULL)
exit(1);
cigar_p1s = (char*** )calloc(thread_n, sizeof(char** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
cigar_p1s[r_i] = (char** )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(char* ));
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if((cigar_p1s[r_i][m] = (char* )calloc(cigar_max_n, 1)) == NULL)
exit(1);
}
xa_d1s = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
xa_d1s[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
lv_re1s = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
lv_re1s[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(int));
#endif
fprintf(stderr, "Load output allocation\n");
op_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_rc[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ops_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_rc[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ref_seq_tmp1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ref_seq_tmp1[r_i] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8);
cov_a_n_s = (uint8_t* )calloc(thread_n, 1);
s_uid_f = (uint8_t* )calloc(thread_n, 1);
seed_l = (int16_t* )calloc(thread_n, 2);//cannot be 0
max_mismatch = (uint8_t* )calloc(thread_n, 1);
max_mismatch_p = (uint8_t* )calloc(thread_n, 1);
dm_op = (int* )calloc(thread_n, 4);
dm_ops = (int* )calloc(thread_n, 4);
low_mask = (uint64_t* )calloc(thread_n, 8);
cigar_m = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
cigar_m[r_i] = (char* )calloc(CIGARMN, 1);
ali_ref_seq = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
ali_ref_seq[r_i] = (char* )calloc(readlen_max + 64, 1);
read_char = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
read_char[r_i] = (char* )calloc(readlen_max + 32, 1);
pos_ren[0][0] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[1][1] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
sub_mask = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
sub_mask[r_i] = (uint16_t* )calloc(33, 2);
ex_d_mask = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ex_d_mask[r_i] = (uint64_t* )calloc(33, 8);
read_bit_1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
read_val_1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
read_val1 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
read_val1[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
read_val1[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
read_val1[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
qual_arr_single = (float** )calloc(thread_n, sizeof(float* ));
for(r_i = 0; r_i < thread_n; r_i++)
qual_arr_single[r_i] = (float* )calloc(readlen_max, sizeof(float ));
#endif
#ifdef PAIR_RANDOM_SEED
seed_r_dup = (uint32_t* )calloc(RANDOM_RANGE, 4);
srand((unsigned)time(0));
pos_r_nr = RANDOM_RANGE;
r_dup_i = 0;
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE_MAX; pos_r_ir++)
if((rand() % (RANDOM_RANGE_MAX - pos_r_ir)) < pos_r_nr)
{
seed_r_dup[r_dup_i++] = pos_r_ir;
pos_r_nr--;
}
random_buffer = (uint32_t* )malloc((RAN_CIR) << 2);
for(pos_r_ir = 0; pos_r_ir < RAN_CIR; pos_r_ir++)
random_buffer[pos_r_ir] = (uint32_t )rand();
#endif
#ifdef READN_RANDOM_SEED
random_buffer_readn = (uint32_t* )calloc(RANDOM_RANGE_READN, 4);
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE_READN; pos_r_ir++)
random_buffer_readn[pos_r_ir] = (uint32_t )rand();
#endif
InitiateLVCompute(L, thread_n);
//for pthread read input
fprintf(stderr, "Load seq input memory\n");
seqio = (seq_io* )calloc(read_in, sizeof(seq_io));
char** read_seq1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
read_seq1_buffer[r_i] = (char* )calloc(readlen_max, 1);
char** name_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
name_buffer[r_i] = (char* )calloc(readlen_name, 1);
qual1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
qual1_buffer[r_i] = (char* )calloc(readlen_max, 1);
#ifdef OUTPUT_ARR
read_rev_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
read_rev_buffer[r_i] = (char* )calloc(readlen_max, 1);
pr_cigar1_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
pr_cigar1_buffer[r_i] = (char* )calloc(cigar_max_n, 1);
chr_res_buffer = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
chr_res_buffer[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
xa_d1s_buffer = (char** )calloc(read_in, sizeof(char* ));
for(r_i = 0; r_i < read_in; r_i++)
xa_d1s_buffer[r_i] = (uint8_t* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
sam_pos1s_buffer = (uint32_t** )calloc(read_in, sizeof(uint32_t* ));
for(r_i = 0; r_i < read_in; r_i++)
sam_pos1s_buffer[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
lv_re1s_buffer = (int** )calloc(read_in, sizeof(int* ));
for(r_i = 0; r_i < read_in; r_i++)
lv_re1s_buffer[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
#endif
#ifdef KSW_ALN
ali_ref_seq2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
ali_ref_seq2[r_i] = (char* )calloc(readlen_max + 64, 1);
read_char2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
read_char2[r_i] = (char* )calloc(readlen_max + 32, 1);
op_dm_kl1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_kl1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_kr1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_kr1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_kl1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_kl1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_kr1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_kr1[r_i] = (int* )calloc(cus_max_output_ali, 4);
int8_t l, k1;
mat = (int8_t*)calloc(25, sizeof(int8_t));
for (l = k1 = 0; l < 4; ++l)
{
for (m = 0; m < 4; ++m) mat[k1++] = l == m ? 1 : -4; /* weight_match : -weight_mismatch */
mat[k1++] = -1; // ambiguous base
}
for (m = 0; m < 5; ++m) mat[k1++] = 0;
#endif
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
qual_filt_lv1 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
qual_filt_lv1[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
qual_filt_lv1[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
qual_filt_lv1[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
#endif
#ifdef ALTER_DEBUG_SINGLE_END
seed_length_arr = (seed_length_array** )calloc(thread_n, sizeof(seed_length_array* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_length_arr[r_i] = (seed_length_array* )calloc(cus_max_output_ali, sizeof(seed_length_array));
rep_go = (uint8_t* )calloc(thread_n, 1);
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
mp_subs1 = (float*** )calloc(thread_n, sizeof(float** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
mp_subs1[r_i] = (float** )calloc(2, sizeof(float* ));
mp_subs1[r_i][0] = (float* )calloc(readlen_max, sizeof(float));
mp_subs1[r_i][1] = (float* )calloc(readlen_max, sizeof(float));
}
sub_t = (float* )calloc(thread_n, sizeof(float ));
#endif
end = clock();
t = (double)(end - start) / CLOCKS_PER_SEC;
fprintf(stderr, "%lf seconds is used for allocating memory\n", t);
fprintf(stderr, "begin reading fastq single-end reads and doing seed reduction and alignment\n");
#ifdef R_W_LOCK
pthread_rwlock_init(&rwlock, NULL);
int seqii_i = 0;
#endif
double dtime = omp_get_wtime(); //value in seconds
while (kr1 >= 0)
{
for(seqii = 0; (seqii < read_in) && ((kr1 = kseq_read(seq1)) > 0); seqii++) //(kr1 >= 0)
{
strncpy(name_buffer[seqii], seq1->name.s, seq1->name.l);
if((seq1->name.s)[seq1->name.l - 2] == '/')
name_buffer[seqii][seq1->name.l - 2] = '\0';
else name_buffer[seqii][seq1->name.l] = '\0';
if(seq1->seq.l > readlen_max)
{
seqio[seqii].read_length1 = readlen_max;
seqio[seqii].length_h1 = seq1->seq.l - readlen_max;
}
else
{
seqio[seqii].read_length1 = seq1->seq.l;
seqio[seqii].length_h1 = 0;
}
read_length_tmp = seqio[seqii].read_length1;
strncpy(read_seq1_buffer[seqii], seq1->seq.s, read_length_tmp);
read_seq1_buffer[seqii][read_length_tmp] = '\0';
strncpy(qual1_buffer[seqii], seq1->qual.s, read_length_tmp);
qual1_buffer[seqii][read_length_tmp] = '\0';
seqio[seqii].read_seq1 = read_seq1_buffer[seqii];
seqio[seqii].name = name_buffer[seqii];
seqio[seqii].qual1 = qual1_buffer[seqii];
}
if(thread_n <= 1)
{
#ifdef R_W_LOCK
for(seqii_i = 0; seqii_i < seqii; seqii_i++)
seed_ali_core_single_end(seqii_i, 0);
#else
seed_ali_core_single_end(seqii, 0);
#endif
}
else
{
pthread_t* tid;
thread_ali_t* data;
pthread_attr_t attr;
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
data = (thread_ali_t* )calloc(thread_n, sizeof(thread_ali_t ));
tid = (pthread_t* )calloc(thread_n, sizeof(pthread_t ));
for(r_i = 0; r_i < thread_n; ++r_i)
{
data[r_i].tid = r_i;
data[r_i].seqn = seqii;
pthread_create(&tid[r_i], &attr, worker_single_end, data + r_i);
}
for(r_i = 0; r_i < thread_n; ++r_i) pthread_join(tid[r_i], 0);
free(data);
free(tid);
}
//output
#ifdef OUTPUT_ARR
for(seqi = 0; seqi < seqii; seqi++)
{
if(seqio[seqi].length_h1 == 0)
{
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s\t*\t0\t0\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, seqio[seqi].seq1,
seqio[seqi].qual1
);
if(seqio[seqi].xa_n > 0)
{
fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n; v_cnt_i++)
fprintf(fp_sam, "%s,%c%u,%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d1s[v_cnt_i], seqio[seqi].sam_pos1s[v_cnt_i], seqio[seqi].cigar_p1s[v_cnt_i], seqio[seqi].lv_re1s[v_cnt_i]);
}
fprintf(fp_sam, "\tNM:i:%u\n",seqio[seqi].nm1);
}
else
{
sprintf(h_chars, "%uH", seqio[seqi].length_h1);
fprintf(fp_sam, "%s\t%u\t%s\t%"PRId64"\t%d\t%s%s\t*\t0\t0\t%s\t%s",
seqio[seqi].name, seqio[seqi].flag1, chr_names[seqio[seqi].chr_re], seqio[seqi].pos1,
seqio[seqi].qualc1, seqio[seqi].cigar1, h_chars, seqio[seqi].seq1,
seqio[seqi].qual1
);
if(seqio[seqi].xa_n > 0)
{
fprintf(fp_sam, "\tXA:Z:");
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n; v_cnt_i++)
{
fprintf(fp_sam, "%s,%c%u,%s%s,%d;",chr_names[seqio[seqi].chr_res[v_cnt_i]], seqio[seqi].xa_d1s[v_cnt_i], seqio[seqi].sam_pos1s[v_cnt_i], seqio[seqi].cigar_p1s[v_cnt_i], h_chars, seqio[seqi].lv_re1s[v_cnt_i]);
}
}
fprintf(fp_sam, "\tNM:i:%u\n",seqio[seqi].nm1);
}
}
#endif
#ifdef OUTPUT_ARR
for(seqi = 0; seqi < seqii; seqi++)
{
if(seqio[seqi].xa_n > 0) //
{
for(v_cnt_i = 0; v_cnt_i < seqio[seqi].xa_n; v_cnt_i++)
{
free(seqio[seqi].cigar_p1s[v_cnt_i]);
}
}
}
#endif
}
dtime = omp_get_wtime() - dtime;
fprintf(stderr, "%lf seconds is used \n", dtime);
fflush(stdout);
#ifdef R_W_LOCK
pthread_rwlock_destroy(&rwlock);
#endif
#ifdef PTHREAD_USE
if(g_low != NULL) free(g_low);
if(r_low != NULL) free(r_low);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedm[r_i] != NULL) free(seedm[r_i]);
if(seedm != NULL) free(seedm);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedu[r_i] != NULL) free(seedu[r_i]);
if(seedu != NULL) free(seedu);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedsets[r_i] != NULL) free(seedsets[r_i]);
if(seedsets != NULL) free(seedsets);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_off[r_i] != NULL) free(seed_set_off[r_i]);
if(seed_set_off != NULL) free(seed_set_off);
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_set_pos_single[r_i] != NULL) free(seed_set_pos_single[r_i]);
if(seed_set_pos_single != NULL) free(seed_set_pos_single);
if(set_pos_n_single != NULL) free(set_pos_n_single);
if(spa_i_single != NULL) free(spa_i_single);
for(r_i = 0; r_i < thread_n; r_i++)
if(seedpa1_single[r_i] != NULL) free(seedpa1_single[r_i]);
if(seedpa1_single != NULL) free(seedpa1_single);
#ifdef SINGLE_PAIR
if(cov_num_front_single != NULL) free(cov_num_front_single);
if(cov_num_re_single != NULL) free(cov_num_re_single);
#endif
for(r_i = 0; r_i < thread_n; r_i++)
if(pos_add[r_i] != NULL) free(pos_add[r_i]);
if(pos_add != NULL) free(pos_add);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_vector_pos1[r_i] != NULL) free(op_vector_pos1[r_i]);
if(op_vector_pos1 != NULL) free(op_vector_pos1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_vector_pos1[r_i] != NULL) free(ops_vector_pos1[r_i]);
if(ops_vector_pos1 != NULL) free(ops_vector_pos1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_l1[r_i] != NULL) free(op_dm_l1[r_i]);
if(op_dm_l1 != NULL) free(op_dm_l1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_r1[r_i] != NULL) free(op_dm_r1[r_i]);
if(op_dm_r1 != NULL) free(op_dm_r1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_l1[r_i] != NULL) free(ops_dm_l1[r_i]);
if(ops_dm_l1 != NULL) free(ops_dm_l1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_r1[r_i] != NULL) free(ops_dm_r1[r_i]);
if(ops_dm_r1 != NULL) free(ops_dm_r1);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < cus_max_output_ali; m++)
if(op_vector_seq1[r_i][m] != NULL) free(op_vector_seq1[r_i][m]);
if(op_vector_seq1[r_i] != NULL) free(op_vector_seq1[r_i]);
}
if(op_vector_seq1 != NULL) free(op_vector_seq1);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < cus_max_output_ali; m++)
if(ops_vector_seq1[r_i][m] != NULL) free(ops_vector_seq1[r_i][m]);
if(ops_vector_seq1[r_i] != NULL) free(ops_vector_seq1[r_i]);
}
if(ops_vector_seq1 != NULL) free(ops_vector_seq1);
#ifdef ALT_ALL
for(r_i = 0; r_i < thread_n; r_i++)
if(chr_res[r_i] != NULL) free(chr_res[r_i]);
if(chr_res != NULL) free(chr_res);
for(r_i = 0; r_i < thread_n; r_i++)
if(sam_pos1s[r_i] != NULL) free(sam_pos1s[r_i]);
if(sam_pos1s != NULL) free(sam_pos1s);
for(r_i = 0; r_i < thread_n; r_i++)
{
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if(cigar_p1s[r_i][m] != NULL) free(cigar_p1s[r_i][m]);
if(cigar_p1s[r_i] != NULL) free(cigar_p1s[r_i]);
}
if(cigar_p1s != NULL) free(cigar_p1s);
for(r_i = 0; r_i < thread_n; r_i++)
if(xa_d1s[r_i] != NULL) free(xa_d1s[r_i]);
if(xa_d1s != NULL) free(xa_d1s);
for(r_i = 0; r_i < thread_n; r_i++)
if(lv_re1s[r_i] != NULL) free(lv_re1s[r_i]);
if(lv_re1s != NULL) free(lv_re1s);
#endif
for(r_i = 0; r_i < thread_n; r_i++)
if(op_rc[r_i] != NULL) free(op_rc[r_i]);
if(op_rc != NULL) free(op_rc);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_rc[r_i] != NULL) free(ops_rc[r_i]);
if(ops_rc != NULL) free(ops_rc);
for(r_i = 0; r_i < thread_n; r_i++)
if(ref_seq_tmp1[r_i] != NULL) free(ref_seq_tmp1[r_i]);
if(ref_seq_tmp1 != NULL) free(ref_seq_tmp1);
if(cov_a_n_s != NULL) free(cov_a_n_s);
if(s_uid_f != NULL) free(s_uid_f);
if(max_mismatch != NULL) free(max_mismatch);
if(max_mismatch_p != NULL) free(max_mismatch_p);
if(dm_op != NULL) free(dm_op);
if(dm_ops != NULL) free(dm_ops);
if(low_mask != NULL) free(low_mask);
for(r_i = 0; r_i < thread_n; r_i++)
if(cigar_m[r_i] != NULL) free(cigar_m[r_i]);
if(cigar_m != NULL) free(cigar_m);
for(r_i = 0; r_i < thread_n; r_i++)
if(ali_ref_seq[r_i] != NULL) free(ali_ref_seq[r_i]);
if(ali_ref_seq != NULL) free(ali_ref_seq);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_char[r_i] != NULL) free(read_char[r_i]);
if(read_char != NULL) free(read_char);
if(pos_ren[0][0] != NULL) free(pos_ren[0][0]);
if(pos_ren[1][1] != NULL) free(pos_ren[1][1]);
for(r_i = 0; r_i < thread_n; r_i++)
if(sub_mask[r_i] != NULL) free(sub_mask[r_i]);
if(sub_mask != NULL) free(sub_mask);
for(r_i = 0; r_i < thread_n; r_i++)
if(ex_d_mask[r_i] != NULL) free(ex_d_mask[r_i]);
if(ex_d_mask != NULL) free(ex_d_mask);
if(read_bit_1 != NULL) free(read_bit_1);
if(read_val_1 != NULL) free(read_val_1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if(read_val1[r_i][0] != NULL) free(read_val1[r_i][0]);
if(read_val1[r_i][1] != NULL) free(read_val1[r_i][1]);
if(read_val1[r_i] != NULL) free(read_val1[r_i]);
}
if(read_val1 != NULL) free(read_val1);
for(r_i = 0; r_i < thread_n; r_i++)
if(qual_arr_single[r_i] != NULL) free(qual_arr_single[r_i]);
if(qual_arr_single != NULL) free(qual_arr_single);
#endif
#ifdef PAIR_RANDOM_SEED
if(seed_r_dup != NULL) free(seed_r_dup);
if(random_buffer != NULL) free(random_buffer);
#endif
#ifdef READN_RANDOM_SEED
if(random_buffer_readn) free(random_buffer_readn);
#endif
if(seqio != NULL) free(seqio);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_seq1_buffer[r_i] != NULL) free(read_seq1_buffer[r_i]);
if(read_seq1_buffer != NULL) free(read_seq1_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(name_buffer[r_i] != NULL) free(name_buffer[r_i]);
if(name_buffer != NULL) free(name_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(qual1_buffer[r_i] != NULL) free(qual1_buffer[r_i]);
if(qual1_buffer != NULL) free(qual1_buffer);
#ifdef OUTPUT_ARR
for(r_i = 0; r_i < thread_n; r_i++)
if(read_rev_buffer[r_i] != NULL) free(read_rev_buffer[r_i]);
if(read_rev_buffer != NULL) free(read_rev_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(pr_cigar1_buffer[r_i] != NULL) free(pr_cigar1_buffer[r_i]);
if(pr_cigar1_buffer != NULL) free(pr_cigar1_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(chr_res_buffer[r_i] != NULL) free(chr_res_buffer[r_i]);
if(chr_res_buffer != NULL) free(chr_res_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(xa_d1s_buffer[r_i] != NULL) free(xa_d1s_buffer[r_i]);
if(xa_d1s_buffer != NULL) free(xa_d1s_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(sam_pos1s_buffer[r_i] != NULL) free(sam_pos1s_buffer[r_i]);
if(sam_pos1s_buffer != NULL) free(sam_pos1s_buffer);
for(r_i = 0; r_i < thread_n; r_i++)
if(lv_re1s_buffer[r_i] != NULL) free(lv_re1s_buffer[r_i]);
if(lv_re1s_buffer != NULL) free(lv_re1s_buffer);
#endif
#ifdef KSW_ALN
for(r_i = 0; r_i < thread_n; r_i++)
if(ali_ref_seq2[r_i] != NULL) free(ali_ref_seq2[r_i]);
if(ali_ref_seq2 != NULL) free(ali_ref_seq2);
for(r_i = 0; r_i < thread_n; r_i++)
if(read_char2[r_i] != NULL) free(read_char2[r_i]);
if(read_char2 != NULL) free(read_char2);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_kl1[r_i] != NULL) free(op_dm_kl1[r_i]);
if(op_dm_kl1 != NULL) free(op_dm_kl1);
for(r_i = 0; r_i < thread_n; r_i++)
if(op_dm_kr1[r_i] != NULL) free(op_dm_kr1[r_i]);
if(op_dm_kr1 != NULL) free(op_dm_kr1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_kl1[r_i] != NULL) free(ops_dm_kl1[r_i]);
if(ops_dm_kl1 != NULL) free(ops_dm_kl1);
for(r_i = 0; r_i < thread_n; r_i++)
if(ops_dm_kr1[r_i] != NULL) free(ops_dm_kr1[r_i]);
if(ops_dm_kr1 != NULL) free(ops_dm_kr1);
free(mat);
#endif
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
for(r_i = 0; r_i < thread_n; r_i++)
{
if(qual_filt_lv1[r_i][0] != NULL) free(qual_filt_lv1[r_i][0]);
if(qual_filt_lv1[r_i][1] != NULL) free(qual_filt_lv1[r_i][1]);
if(qual_filt_lv1[r_i] != NULL) free(qual_filt_lv1[r_i]);
}
if(qual_filt_lv1 != NULL) free(qual_filt_lv1);
#endif
#ifdef ALTER_DEBUG_SINGLE_END
for(r_i = 0; r_i < thread_n; r_i++)
if(seed_length_arr[r_i] != NULL) free(seed_length_arr[r_i]);
if(seed_length_arr != NULL) free(seed_length_arr);
if(rep_go != NULL) free(rep_go);
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
for(r_i = 0; r_i < thread_n; r_i++)
{
if(mp_subs1[r_i][0] != NULL) free(mp_subs1[r_i][0]);
if(mp_subs1[r_i][1] != NULL) free(mp_subs1[r_i][1]);
if(mp_subs1[r_i] != NULL) free(mp_subs1[r_i]);
}
if(sub_t != NULL) free(sub_t);
#endif
fclose(fp_sam);
kseq_destroy(seq1);
gzclose(fp1);
return 0;
}
#ifdef R_W_LOCK
int seed_ali_core_single_end(int read_seq_core, uint8_t tid)
#else
int seed_ali_core_single_end(uint32_t seqn, uint8_t tid)
#endif
{
uint16_t dm_i = 0;
uint8_t extension_stop = 0;
char cigar_p1[MAX_LV_CIGAR];
uint8_t rc_i = 0;
uint8_t lv_ref_length_re = 0;
uint8_t q_n1 = 0;
uint8_t c_m_f = 0;
uint8_t end1_uc_f = 0;
uint8_t nuc1_f = 0;
uint8_t b_t_n_r = 0;
uint8_t re_d = 0;
uint16_t f_cigar[MAX_LV_CIGAR];
char sam_seq1[MAX_READLEN + 1] = {};
char cigarBuf1[MAX_LV_CIGAR] = {};
char cigarBuf2[MAX_LV_CIGAR] = {};
char str_o[MAX_LV_CIGAR];
char b_cigar[MAX_LV_CIGAR];
char* pch = NULL;
char* saveptr = NULL;
uint16_t ref_copy_num = 0;
uint16_t f_cigarn = 0;
uint16_t read_bit_char = 0;
uint16_t rst_i = 0;
uint16_t s_m_t = 0;
uint16_t read_b_i = 0;
uint16_t f_c = 0;
uint16_t pchl = 0;
uint16_t f_i = 0;
uint16_t s_o = 0;
uint16_t snt = 0;
uint16_t d_n1 = 0;
uint16_t i_n1 = 0;
uint16_t read_length = 0;
uint16_t lv_k = 0;
uint32_t read_length_a = 0;
uint32_t seqi = 0;
uint32_t v_cnt = 0;
uint32_t vs_cnt = 0;
uint32_t ref_copy_num_chars = 0;
uint32_t r_i = 0;
uint32_t psp_i = 0;
uint32_t d_l1 = 0;
uint32_t d_r1 = 0;
uint32_t mis_c_n = 0;
uint32_t xa_i = 0;
uint32_t v_cnt_i = 0;
uint32_t va_cnt_i = 0;
uint32_t sam_flag1 = 0;
uint32_t seed1_i = 0;
uint32_t sam_seq_i = 0;
uint32_t max_single_score = 0;
uint32_t seed_posn_filter_single = 0;
int s_r_o_l1 = 0;
int s_r_o_r1 = 0;
int lv_re1f = 0;
int sam_qual1 = 0;
int chr_re = 0;
int mid = 0;
int low = 0;
int high = 0;
int m_m_n = 0;
int sn = 0;
int bit_char_i = 0;
int dm1 = 0;
int dm_l1 = 0;
int dm_r1 = 0;
int dmt1 = 0;
int lv_dmt1 = 0;
int ld1 = 0;
int rd1 = 0;
int cmp_re = 0;
int q_rear_i = 0;
int q_rear1 = 0;
int cache_dml1[MAX_Q_NUM];
int cache_dmr1[MAX_Q_NUM];
int cache_dis1[MAX_Q_NUM];
int cache_kl1[MAX_Q_NUM];
int cache_kr1[MAX_Q_NUM];
uint16_t off_i = 0;
uint16_t max_sets_n = 0;
uint16_t max_seed_length[2];
uint64_t c_tmp = 0;
uint64_t xor_tmp = 0;
uint64_t ref_tmp_ori = 0;
uint64_t ref_tmp_ori2 = 0;
uint64_t tran_tmp_p = 0;
uint64_t tran_tmp = 0;
int64_t sam_pos1 = 0;
uint64_t cache_end1[MAX_Q_NUM][MAX_REF_SEQ_C];
seed_pa_single* seed_pr1 = NULL;
uint16_t s_offset1 = 0;
int16_t s_r_o_l = 0;
int16_t s_r_o_r = 0;
#ifdef KSW_ALN
int band_with = 33;//100
int zdrop = 0;//100
int end_bonus = 5;
int tle;
int gtle;
int gscore;
int max_off;
int x_score, y_score, op_score, len_score, op_score1, len_score1, op_score2, len_score2;
int k_start1 = 0;
int k_start2 = 0;
int k_middle = 0;
uint32_t* cigar1 = NULL;
uint32_t* cigar2 = NULL;
int n_cigar1 = 0;
int n_cigar2 = 0;
int nm_score = 0;
#endif
#ifdef QUAL_FILT_SINGLE_END
uint64_t* qual_filt_1 = NULL;
uint8_t qual_filt_fix_single_end = 55;//
#endif
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
uint8_t* qual_filt_lv_1 = NULL;
uint8_t* qual_filt_lv_1_o = NULL;
#endif
#ifdef ALTER_DEBUG_SINGLE_END
uint16_t seed_length1 = 0;
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
float log_tmp = 0;
float* mp_subs_1 = NULL;
float* mp_subs_1_o = NULL;
float m_sub_tmp = 0;
#endif
uint8_t mp_flag = 0;
uint8_t cir_n = 0;
uint16_t mis_c_n_filt = 0;
int16_t dm_cir_min = 0;
#ifdef UNPIPATH_OFF_K20
uint64_t posi = 0;
uint64_t pos_l = 0;
uint64_t x = 0;
#else
uint32_t posi = 0;
uint32_t pos_l = 0;
uint32_t x = 0;
#endif
#ifdef READN_RANDOM_SEED
char tmp_char;
uint16_t readn_re1 = 0;
uint16_t readn_re2 = 0;
#endif
#ifdef CIGAR_LEN_ERR
int cigar_len = 0;
int cigar_len_tmp = 0;
int cigar_len_re = 0;
uint16_t pchl_tmp = 0;
uint16_t s_o_tmp = 0;
char* pch_tmp = NULL;
char* saveptr_tmp = NULL;
char cigar_tmp[MAX_LV_CIGARCOM];
#endif
#ifndef R_W_LOCK
for(seqi = 0; seqi < seqn; seqi++)
#else
if(1)
#endif
{
#ifndef R_W_LOCK
#ifdef PTHREAD_USE
if ((seqi % thread_n) != tid) continue;
#endif
#else
seqi = read_seq_core;
#endif
read_length = seqio[seqi].read_length1;
lv_k = (read_length * max_single_score_r) + 1;
read_length_a = read_length - 1;
#ifdef SINGLE_PAIR
cov_num_front_single[tid] = (read_length_a >> 7);
cov_num_re_single[tid] = 63 - ((read_length_a >> 1) & 0X3f);
#endif
f_cigarn = read_length;
f_cigar[f_cigarn] = '\0';
//sprintf(cigar_m[tid],"%uM\0",read_length);
sprintf(cigar_m[tid],"%uM",read_length);
//for bit operation
read_bit_char = (((uint16_t )((read_length_a >> 5) + 1)) << 3);
ref_copy_num = ((read_length_a) >> 5) + 3;
ref_copy_num_chars = (ref_copy_num << 3);
lv_ref_length_re = (read_length & 0X1f);
for(r_i = 0; r_i <= 32 - lv_ref_length_re; r_i++)
{
ex_d_mask[tid][r_i] = bit_assi[lv_ref_length_re + r_i];
sub_mask[tid][r_i] = ref_copy_num - 2;
}
for(r_i = 33 - lv_ref_length_re; r_i <= 32; r_i++)
{
ex_d_mask[tid][r_i] = bit_assi[lv_ref_length_re + r_i - 32];
sub_mask[tid][r_i] = ref_copy_num - 1;
}
low_mask[tid] = bit_assi[lv_ref_length_re];
#ifdef QUAL_FILT_SINGLE_END
memset(qual_filt1[tid][0], 0, read_bit_char);
memset(qual_filt1[tid][1], 0, read_bit_char);
c_tmp = 3;
for(r_i = 0; r_i < read_length; r_i++)
{
if(seqio[seqi].qual1[r_i] < qual_filt_fix_single_end) //'7': 55 63
{
qual_filt1[tid][0][r_i >> 5] |= (((uint64_t )c_tmp) << ((31 - (r_i & 0X1f)) << 1));
qual_filt1[tid][1][(read_length_a - r_i) >> 5] |= (((uint64_t )c_tmp) << ((31 - ((read_length_a - r_i) & 0X1f)) << 1));
}
}
for(r_i = 0; r_i < (read_length >> 5) + 1; r_i++)
qual_filt1[tid][0][r_i] = ~qual_filt1[tid][0][r_i];
for(r_i = 0; r_i < (read_length >> 5) + 1; r_i++)
qual_filt1[tid][1][r_i] = ~qual_filt1[tid][1][r_i];
#endif
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
for(r_i = 0; r_i < read_length; r_i++)
{
if(seqio[seqi].qual1[r_i] < qual_filt_fix_single_end) qual_filt_lv1[tid][0][r_i] = 0;
else qual_filt_lv1[tid][0][r_i] = 3;
}
for(r_i = 0; r_i < read_length; r_i++)
{
if(seqio[seqi].qual1[r_i] < qual_filt_fix_single_end) qual_filt_lv1[tid][1][read_length_a - r_i] = 0;
else qual_filt_lv1[tid][1][read_length_a - r_i] = 3;
}
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
for(r_i = 0; r_i < read_length; r_i++)
{
m_sub_tmp = mp_sub_bp[seqio[seqi].qual1[r_i]];
mp_subs1[tid][0][r_i] = m_sub_tmp;
mp_subs1[tid][1][read_length_a - r_i] = m_sub_tmp;
}
#endif
max_single_score = (uint32_t )(((float )read_length) * max_single_score_r);
cov_a_n_s[tid] = ((read_length_a) >> 6) + 1;
max_mismatch[tid] = (uint8_t )(((float )read_length) * mis_match_r);
max_mismatch_p[tid] = max_mismatch[tid] - 1;
memset(read_bit1[tid][0], 0, read_bit_char);
memset(read_bit1[tid][1], 0, read_bit_char);
r_i = 0;
while ((seqio[seqi].read_seq1)[r_i])
{
#ifdef READN_RANDOM_SEED
tmp_char = (seqio[seqi].read_seq1)[r_i];
if(tmp_char == 'N')
{
readn_re1 = readn_cnt & 0X3ff;
readn_re2 = readn_cnt & 0Xf;
c_tmp = ((random_buffer_readn[readn_re1] >> (readn_re2 << 1)) & 0X3);
readn_cnt++;
}
else c_tmp = charToDna5n[tmp_char];
#else
c_tmp = charToDna5n[(seqio[seqi].read_seq1)[r_i]];
#endif
#ifdef ALI_LV
read_val1[tid][0][r_i] = c_tmp;
read_val1[tid][1][read_length_a - r_i] = c_tmp ^ 0X3;
#endif
read_bit1[tid][0][r_i >> 5] |= (((uint64_t )c_tmp) << ((31 - (r_i & 0X1f)) << 1));
read_bit1[tid][1][(read_length_a - r_i) >> 5] |= (((uint64_t )(c_tmp ^ 0X3)) << ((31 - ((read_length_a - r_i) & 0X1f)) << 1));
r_i++;
}
seed_l[tid] = seed_l_max;
#ifdef ALTER_DEBUG_SINGLE_END
rep_go[tid] = 1;
#endif
cir_n = 1;
while(cir_n <= cir_fix_n)
{
cir_cnt++;
dm_op[tid] = MAX_OP_SCORE;
dm_ops[tid] = MAX_OP_SCORE;
v_cnt = 0;
vs_cnt = 0;
dm_cir_min = 0Xfff;
spa_i_single[tid] = 0;
set_pos_n_single[tid] = 0;
for(rc_i = 0; rc_i < 2; rc_i++)
{
max_seed_length[rc_i] = 0;
#ifdef UNPIPATH_OFF_K20
single_seed_reduction_core_single64(seedpa1_single[tid], read_bit1[tid][rc_i], read_val1[tid][rc_i], &(seed_set_pos_single[tid]), tid, read_length, &(max_seed_length[rc_i]), rc_i);
#else
single_seed_reduction_core_single(seedpa1_single[tid], read_bit1[tid][rc_i], read_val1[tid][rc_i], &(seed_set_pos_single[tid]), tid, read_length, &(max_seed_length[rc_i]), rc_i);
#endif
}
if(spa_i_single[tid] == 0)
{
seed_l[tid] -= seed_step;
}
else
{
seed_posn_filter_single = 0;
extension_stop = 0;
seed_pr1 = seedpa1_single[tid];
qsort(seed_pr1, spa_i_single[tid], sizeof(seed_pa_single), compare_plen_single);
max_sets_n = (max_seed_length[0] > max_seed_length[1]) ? max_seed_length[0]:max_seed_length[1];
for(off_i = 0; off_i < spa_i_single[tid]; off_i++)
if(seed_pr1[off_i].length < max_sets_n >> 1)
{
++off_i;
break;
}
for(seed1_i = 0; (seed1_i < off_i) && (extension_stop == 0); seed1_i++) //
{
rc_i = seed_pr1[seed1_i].rc;
read_bit_1[tid] = read_bit1[tid][rc_i];
#ifdef QUAL_FILT_SINGLE_END
qual_filt_1 = qual_filt1[tid][rc_i];
#endif
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][rc_i];
qual_filt_lv_1_o = qual_filt_lv1[tid][1 - rc_i];
#endif
if(seed_pr1[seed1_i].ui == 1)
{
end1_uc_f = 0;
nuc1_f = 0;
d_l1 = seed_pr1[seed1_i].ref_pos_off;
d_r1 = seed_pr1[seed1_i].ref_pos_off_r;
}
else
{
end1_uc_f = 1;
}
q_rear1 = 0;
q_n1 = 0;
dmt1 = ali_exl;
lv_dmt1 = lv_k;
s_r_o_l1 = seed_pr1[seed1_i].s_r_o_l;
s_r_o_r1 = seed_pr1[seed1_i].s_r_o_r;
#ifdef ALTER_DEBUG_SINGLE_END
seed_length1 = seed_pr1[seed1_i].length;
#endif
for(psp_i = 0; psp_i < seed_pr1[seed1_i].pos_n; psp_i++)
{
if(seed_posn_filter_single > seed_filter_pos_num_singlen) extension_stop = 1;//break;
seed_posn_filter_single++;
posi = seed_set_pos_single[tid][seed_pr1[seed1_i].pos_start + psp_i];
extension_cnt++;
//for end1
if((end1_uc_f == 0) && ((dmt1 <= d_l1) && (dmt1 <= d_r1))) // && (nuc1_f == 0)
{
if(nuc1_f == 0)
{
pos_l = posi - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars);
for(rst_i = 0; rst_i < ref_copy_num - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask[tid];
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num - 1] &= low_mask[tid];
}
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT_SINGLE_END
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num - 2];
ref_seq_tmp1[tid][ref_copy_num - 2] &= low_mask[tid];
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT_SINGLE_END
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch[tid]) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch[tid]) break;
#endif
}
ref_seq_tmp1[tid][ref_copy_num - 2] = ref_tmp_ori;
//lv
if(mis_c_n_filt > max_mismatch[tid])
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(s_r_o_l1 + 1, read_char[tid], 33 + s_r_o_l1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_l1, &tle, >le, &gscore, &max_off);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(read_length - s_r_o_r1, read_char[tid], 32 + read_length - s_r_o_r1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_r1, &tle, >le, &gscore, &max_off);
dm1 = MAX_OP_SCORE - (dm_l1 + dm_r1);
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
#ifdef SPLIT_LV_SINGLE
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance_mis(ali_ref_seq[tid], 33 + s_r_o_l1, read_char[tid], s_r_o_l1 + 1, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length_a - s_r_o_l1);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r1, read_char[tid], read_length - s_r_o_r1, lv_dmt1, L[tid], qual_filt_lv_1 + s_r_o_r1);
dm1 = dm_l1 + dm_r1;
#else
//split lv
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + s_r_o_l1, read_char[tid], s_r_o_l1 + 1, lv_dmt1, L[tid]);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + read_length - s_r_o_r1, read_char[tid], read_length - s_r_o_r1, lv_dmt1, L[tid]);
dm1 = dm_l1 + dm_r1;
#endif
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
}
else
{
dm1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1)) //need to be modified
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch_p[tid])
{
dmt1 = 0;
}
}
else
{
dm1 = MAX_EDIT_SCORE;
}
nuc1_f = 1;
}
}
else
{
pos_l = posi - max_extension_length - 1;
re_d = pos_l & 0X1f;
b_t_n_r = 32 - re_d;
if(re_d != 0)
{
tran_tmp_p = (buffer_ref_seq[pos_l >> 5] & bit_tran_re[re_d]);
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5) + 1, ref_copy_num_chars);
for(rst_i = 0; rst_i < ref_copy_num - 1; rst_i++)
{
tran_tmp = (ref_seq_tmp1[tid][rst_i] & bit_tran_re[re_d]);
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
tran_tmp_p = tran_tmp;
}
ref_seq_tmp1[tid][rst_i] >>= (b_t_n_r << 1);
ref_seq_tmp1[tid][rst_i] |= (tran_tmp_p << (re_d << 1));
//clear the lowest n bit
ref_seq_tmp1[tid][rst_i] &= low_mask[tid];
}
else
{
memcpy(ref_seq_tmp1[tid], buffer_ref_seq + (pos_l >> 5), ref_copy_num_chars);
//clear the lowest n bit
ref_seq_tmp1[tid][ref_copy_num - 1] &= low_mask[tid];
}
//trim the beginning and end of the current ref seq based on current minimum edit distance dm_t
s_m_t = sub_mask[tid][dmt1];
ref_seq_tmp1[tid][0] &= bit_tran[dmt1];
ref_seq_tmp1[tid][s_m_t] &= ex_d_mask[tid][dmt1];
//traverse and check whether there is an existing seq that is as same as current new ref seq
c_m_f = 0;
for(q_rear_i = q_rear1 - 1; q_rear_i >= 0; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask[tid][dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
#ifdef KSW_ALN
dm_l1 = cache_kl1[q_rear_i];
dm_r1 = cache_kr1[q_rear_i];
#endif
c_m_f = 1;
break;
}
}
if((q_n1 > MAX_Q_NUM) && (q_rear_i < 0))
{
for(q_rear_i = MAX_Q_NUM - 1; q_rear_i >= q_rear1; q_rear_i--)
{
ref_tmp_ori = cache_end1[q_rear_i][0];
cache_end1[q_rear_i][0] &= bit_tran[dmt1];
ref_tmp_ori2 = cache_end1[q_rear_i][s_m_t];
cache_end1[q_rear_i][s_m_t] &= ex_d_mask[tid][dmt1];
cmp_re = memcmp(cache_end1[q_rear_i], ref_seq_tmp1[tid], (s_m_t + 1) << 3);
cache_end1[q_rear_i][0] = ref_tmp_ori;
cache_end1[q_rear_i][s_m_t] = ref_tmp_ori2;
if(cmp_re == 0)
{
//deal with finding an alignment
dm1 = cache_dis1[q_rear_i];
ld1 = cache_dml1[q_rear_i];
rd1 = cache_dmr1[q_rear_i];
#ifdef KSW_ALN
dm_l1 = cache_kl1[q_rear_i];
dm_r1 = cache_kr1[q_rear_i];
#endif
c_m_f = 1;
break;
}
}
}
//do not find the seq in cache, exact match or lv and add into cache
if(c_m_f == 0)
{
//exact match
mis_c_n = 0;
#ifdef QUAL_FILT_SINGLE_END
mis_c_n_filt = 0;
#endif
ref_tmp_ori = ref_seq_tmp1[tid][ref_copy_num - 2];
ref_seq_tmp1[tid][ref_copy_num - 2] &= low_mask[tid];
for(rst_i = 1, read_b_i = 0; rst_i < ref_copy_num - 1; rst_i++, read_b_i++)
{
xor_tmp = ref_seq_tmp1[tid][rst_i] ^ read_bit_1[tid][read_b_i];
#ifdef QUAL_FILT_SINGLE_END
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
xor_tmp &= qual_filt_1[read_b_i];
mis_c_n_filt += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
if(mis_c_n_filt > max_mismatch[tid]) break;
#else
mis_c_n += popcount_3((((xor_tmp & low_bit_mask) << 1) | (xor_tmp & high_bit_mask)));
mis_c_n_filt = mis_c_n;
if(mis_c_n > max_mismatch[tid]) break;
#endif
}
ref_seq_tmp1[tid][ref_copy_num - 2] = ref_tmp_ori;
//lv
if(mis_c_n_filt > max_mismatch[tid])
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(s_r_o_l1 + 1, read_char[tid], 33 + s_r_o_l1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_l1, &tle, >le, &gscore, &max_off);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_extend(read_length - s_r_o_r1, read_char[tid], 32 + read_length - s_r_o_r1, ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, end_bonus, zdrop, s_r_o_r1 - s_r_o_l1, &dm_r1, &tle, >le, &gscore, &max_off);
dm1 = MAX_OP_SCORE - (dm_l1 + dm_r1);
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
else
{
#ifdef SPLIT_LV_SINGLE
#ifdef QUAL_FILT_LV_MIS_SINGLE_END
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance_mis(ali_ref_seq[tid], 33 + s_r_o_l1, read_char[tid], s_r_o_l1 + 1, lv_dmt1, L[tid], qual_filt_lv_1_o + read_length_a - s_r_o_l1);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r1, read_char[tid], read_length - s_r_o_r1, lv_dmt1, L[tid], qual_filt_lv_1 + s_r_o_r1);
dm1 = dm_l1 + dm_r1;
#else
//split lv
for(bit_char_i = s_r_o_l1, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l1, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_l1 = computeEditDistance(ali_ref_seq[tid], 33 + s_r_o_l1, read_char[tid], s_r_o_l1 + 1, lv_dmt1, L[tid]);
for(bit_char_i = s_r_o_r1, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r1, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ref_seq_tmp1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
dm_r1 = computeEditDistance(ali_ref_seq[tid], 32 + read_length - s_r_o_r1, read_char[tid], read_length - s_r_o_r1, lv_dmt1, L[tid]);
dm1 = dm_l1 + dm_r1;
#endif
ld1 = s_r_o_l1;
rd1 = s_r_o_r1;
#endif
}
}
else
{
dm1 = mis_c_n;
ld1 = 0;
rd1 = 0;
dm_l1 = 0;
dm_r1 = 0;
}
//these two values could be different
if((dm_l1 != -1) && (dm_r1 != -1))
{
if(dm1 < dmt1) dmt1 = dm1 + 1;
if(dm1 < lv_dmt1) lv_dmt1 = dm1 + 1;
if(dm1 < max_mismatch_p[tid])
{
dmt1 = 0;
}
}
else
{
dm1 = MAX_EDIT_SCORE;
}
//add the ref sequence at the end of queue
memcpy(cache_end1[q_rear1], ref_seq_tmp1[tid], ref_copy_num_chars);
cache_dis1[q_rear1] = dm1;
cache_dml1[q_rear1] = ld1;
cache_dmr1[q_rear1] = rd1;
#ifdef KSW_ALN
cache_kl1[q_rear1] = dm_l1;
cache_kr1[q_rear1] = dm_r1;
#endif
q_rear1 = ((q_rear1 + 1) & 0X1f);
++q_n1;
//add edit distance
}
}
if(dm1 < dm_cir_min) dm_cir_min = dm1;
if(dm1 < dm_op[tid])
{
#ifdef DM_COPY_SINGLE
for(dm_i = 0; dm_i < v_cnt; dm_i++)
{
ops_vector_pos1[tid][dm_i] = op_vector_pos1[tid][dm_i];
ops_dm_l1[tid][dm_i] = op_dm_l1[tid][dm_i];
ops_dm_r1[tid][dm_i] = op_dm_r1[tid][dm_i];
ops_dm_kl1[tid][dm_i] = op_dm_kl1[tid][dm_i];
ops_dm_kr1[tid][dm_i] = op_dm_kr1[tid][dm_i];
ops_rc[tid][dm_i] = op_rc[tid][dm_i];
#ifdef MAPPING_QUALITY_SINGLE_END
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars);
#else
if(!((op_dm_l1[tid][dm_i] == 0) && (op_dm_r1[tid][dm_i] == 0)))
memcpy(ops_vector_seq1[tid][dm_i], op_vector_seq1[tid][dm_i], ref_copy_num_chars);
#endif
}
vs_cnt = v_cnt;
dm_ops[tid] = dm_op[tid];
#endif
v_cnt = 0;
op_vector_pos1[tid][v_cnt] = posi;
#ifdef MAPPING_QUALITY_SINGLE_END
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#endif
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
#ifdef KSW_ALN
op_dm_kl1[tid][v_cnt] = dm_l1;
op_dm_kr1[tid][v_cnt] = dm_r1;
#endif
#ifdef ALTER_DEBUG_SINGLE_END
seed_length_arr[tid][v_cnt].seed_length = seed_length1;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
op_rc[tid][v_cnt] = ((rc_i << 1) + rc_i);
++v_cnt;
dm_op[tid] = dm1;
}
else if(dm1 == dm_op[tid])
{
if(v_cnt < cus_max_output_ali)
{
op_vector_pos1[tid][v_cnt] = posi;
#ifdef MAPPING_QUALITY_SINGLE_END
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(op_vector_seq1[tid][v_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#endif
op_dm_l1[tid][v_cnt] = ld1;
op_dm_r1[tid][v_cnt] = rd1;
#ifdef KSW_ALN
op_dm_kl1[tid][v_cnt] = dm_l1;
op_dm_kr1[tid][v_cnt] = dm_r1;
#endif
#ifdef ALTER_DEBUG_SINGLE_END
seed_length_arr[tid][v_cnt].seed_length = seed_length1;
seed_length_arr[tid][v_cnt].index = v_cnt;
#endif
op_rc[tid][v_cnt] = ((rc_i << 1) + rc_i);
++v_cnt;
}
}
else if(dm1 < dm_ops[tid])
{
vs_cnt = 0;
ops_vector_pos1[tid][vs_cnt] = posi;
#ifdef MAPPING_QUALITY_SINGLE_END
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#endif
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
#ifdef KSW_ALN
ops_dm_kl1[tid][vs_cnt] = dm_l1;
ops_dm_kr1[tid][vs_cnt] = dm_r1;
#endif
ops_rc[tid][vs_cnt] = ((rc_i << 1) + rc_i);
++vs_cnt;
dm_ops[tid] = dm1;
}
else if(dm1 == dm_ops[tid])
{
if(vs_cnt < cus_max_output_ali)
{
ops_vector_pos1[tid][vs_cnt] = posi;
#ifdef MAPPING_QUALITY_SINGLE_END
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#else
if(!((ld1 == 0) && (rd1 == 0)))
memcpy(ops_vector_seq1[tid][vs_cnt], ref_seq_tmp1[tid], ref_copy_num_chars);
#endif
ops_dm_l1[tid][vs_cnt] = ld1;
ops_dm_r1[tid][vs_cnt] = rd1;
#ifdef KSW_ALN
ops_dm_kl1[tid][vs_cnt] = dm_l1;
ops_dm_kr1[tid][vs_cnt] = dm_r1;
#endif
ops_rc[tid][vs_cnt] = ((rc_i << 1) + rc_i);
++vs_cnt;
}
}
}
}
#ifdef CIR_CONTINUE_SINGLE_END
if(local_ksw)
{
if((dm_cir_min > max_single_score) && (cir_n != cir_fix_n))
{
seed_l[tid] -= seed_step;
cir_n = cir_fix_n;
continue;
}
}
else
{
if(dm_cir_min > max_single_score)
{
seed_l[tid] -= seed_step;
cir_n++;
if(last_circle_rate)
{
lv_k = (read_length * last_circle_rate);
max_single_score = lv_k;
}
continue;
}
}
#else
if((dm_op[tid] > max_single_score) && (cir_n < cir_fix_n))
{
seed_l[tid] -= seed_step;
cir_n++;
continue;
}
#endif
break;
}
cir_n++;
}
//output
if(v_cnt > 0)
{
#ifdef ALTER_DEBUG_SINGLE_END
if(v_cnt > 1) qsort(seed_length_arr[tid], v_cnt, sizeof(seed_length_array), compare_seed_length);
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(v_cnt > 1)
{
sam_qual1 = 0;
mp_flag = 0;
}
else if(vs_cnt == 0)
{
sam_qual1 = 60;
mp_flag = 0;
}
else
{
mp_flag = 1;
}
#endif
v_cnt_i = 0;
#ifdef ALTER_DEBUG_SINGLE_END
if(v_cnt > 1) v_cnt_i = seed_length_arr[tid][v_cnt_i].index;
#endif
x = op_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos1 = op_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
if(op_rc[tid][v_cnt_i] == 0)
{
#ifdef CHAR_CP_SINGLE_END
read_bit_1[tid] = read_bit1[tid][0];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
#endif
sam_flag1 = 0;
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag)
{
mp_subs_1 = mp_subs1[tid][0];
mp_subs_1_o = mp_subs1[tid][1];
}
#endif
}
else
{
#ifdef CHAR_CP_SINGLE_END
read_bit_1[tid] = read_bit1[tid][1];
#else
for(sam_seq_i = 0; sam_seq_i < read_length; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#endif
sam_flag1 = 16;
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag)
{
mp_subs_1 = mp_subs1[tid][1];
mp_subs_1_o = mp_subs1[tid][0];
}
#endif
}
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) sub_t[tid] = 0;
#endif
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_r_o_l = op_dm_l1[tid][v_cnt_i];
s_r_o_r = op_dm_r1[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m[tid]);
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag)
{
for (bit_char_i = 0, read_b_i = 32; bit_char_i < read_length; bit_char_i++, read_b_i++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((op_vector_seq1[tid][v_cnt_i][read_b_i >> 5] >> ((31 - (read_b_i & 0X1f)) << 1)) & 0X3))
{
sub_t[tid] += mp_subs_1[bit_char_i];
}
}
#endif
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kl1[tid][v_cnt_i], read_char[tid], op_dm_kl1[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr1[tid][v_cnt_i], read_char2[tid], op_dm_kr1[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if(n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if(n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if(s_r_o_l >= op_dm_kl1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", s_r_o_l + 1 - op_dm_kl1[tid][v_cnt_i]);
snt += sn;
}
if((s_r_o_l != -1) && (s_r_o_r != read_length))
{
if((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if(op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if(op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) sub_t[tid] += mp_subs_1_o[read_length + n_cigar1 - s_r_o_l - x_score - read_b_i - 2];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if(s_r_o_l == -1)
{
if(op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if(op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) sub_t[tid] += mp_subs_1_o[read_length + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
}
if(read_length - s_r_o_r > op_dm_kr1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", read_length -s_r_o_r - op_dm_kr1[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
if(n_cigar1) free(cigar1);
if(n_cigar2) free(cigar2);
#endif
}
else
{
nm_score = dm_op[tid];
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
#ifdef CHAR_CP_SINGLE_END
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) computeEditDistanceWithCigar_s_mis_left_mp(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1, mp_subs_1_o + read_length - 1 - s_r_o_l, &(sub_t[tid]));
else computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1);
#else
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1);
#endif
#ifdef CHAR_CP_SINGLE_END
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) computeEditDistanceWithCigar_s_mis_mp(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r, mp_subs_1 + s_r_o_r, &(sub_t[tid]));
else computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r);
#else
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r);
#endif
#else
#ifdef CHAR_CP_SINGLE_END
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], mp_subs_1_o + read_length - 1 - s_r_o_l, &(sub_t[tid]));
else computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid]);
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid]);
#endif
#ifdef CHAR_CP_SINGLE_END
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag) computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], mp_subs_1 + s_r_o_r, &(sub_t[tid]));
else computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid]);
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid]);
#endif
#endif
//deal with front and back lv cigar
m_m_n = s_r_o_r - s_r_o_l - 1;
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok (cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
if((s_r_o_l != -1) && (s_r_o_r != read_length))
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if(s_r_o_l == -1)
{
if(b_cigar[pchl] == 'M')
sn = sprintf(cigar_p1, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
else sn = sprintf(cigar_p1, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
else
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
}
#ifdef CIGAR_LEN_ERR
cigar_len = 0;
s_o_tmp = 0;
cigar_len_tmp = 0;
strncpy(cigar_tmp, cigar_p1, snt);
cigar_tmp[snt] = '\0';
pch_tmp = strtok_r(cigar_tmp,"DMIS", &saveptr_tmp);
while (pch_tmp != NULL)
{
pchl_tmp = strlen(pch_tmp);
s_o_tmp += (pchl_tmp + 1);
if(cigar_p1[s_o_tmp - 1] != 'D')
{
cigar_len_tmp = atoi(pch_tmp);
cigar_len += cigar_len_tmp;
}
pch_tmp = strtok_r(NULL, "DMIS", &saveptr_tmp);
}
if(read_length != cigar_len)
{
if(read_length < cigar_len)
{
cigar_len_re = cigar_len_tmp - (cigar_len - read_length);
if(cigar_len_re > 0) sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
else if(cigar_len_re == 0) sprintf(cigar_p1 + snt - sn, "\0");
else strcpy(cigar_p1, cigar_m[tid]);
}
else
{
cigar_len_re = cigar_len_tmp + (read_length - cigar_len);
sprintf(cigar_p1 + snt - sn, "%u%c", cigar_len_re, cigar_p1[snt - 1]);
}
}
#endif
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos1 = sam_pos1 + i_n1 - d_n1 + s_offset1;
}
#ifdef MAPPING_QUALITY_SINGLE_END
if(mp_flag)
{
sam_qual1 = sub_t[tid];
}
#endif
#ifdef OUTPUT_ARR
seqio[seqi].flag1 = sam_flag1;
seqio[seqi].chr_re = chr_re;
seqio[seqi].pos1 = sam_pos1;
strcpy(pr_cigar1_buffer[seqi], cigar_p1);
seqio[seqi].cigar1 = pr_cigar1_buffer[seqi];
seqio[seqi].nm1 = nm_score;
if(sam_flag1 == 0)
{
seqio[seqi].seq1 = seqio[seqi].read_seq1;
}
else
{
#ifdef CHAR_CP_SINGLE_END
for(sam_seq_i = 0; sam_seq_i < read_length; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#endif
strcpy(read_rev_buffer[seqi], sam_seq1);
read_rev_buffer[seqi][read_length] = '\0';
seqio[seqi].seq1 = read_rev_buffer[seqi];
strrev1(qual1_buffer[seqi]);
}
#endif
}
xa_i = 0;
for(va_cnt_i = 1; va_cnt_i < v_cnt; va_cnt_i++)
{
#ifdef ALTER_DEBUG_SINGLE_END
v_cnt_i = seed_length_arr[tid][va_cnt_i].index;
#else
v_cnt_i = va_cnt_i;
#endif
x = op_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos1 = op_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
chr_res[tid][xa_i] = chr_re;
if(op_rc[tid][v_cnt_i] == 0)
{
#ifdef CHAR_CP_SINGLE_END
read_bit_1[tid] = read_bit1[tid][0];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
}
else
{
#ifdef CHAR_CP_SINGLE_END
read_bit_1[tid] = read_bit1[tid][1];
#else
for(sam_seq_i = 0; sam_seq_i < read_length; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#endif
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
}
d_n1 = 0;
i_n1 = 0;
lv_re1f = dm_op[tid];
s_offset1 = 0;
s_r_o_l = op_dm_l1[tid][v_cnt_i];
s_r_o_r = op_dm_r1[tid][v_cnt_i];
if((s_r_o_l == 0) && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m[tid]);
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < op_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kl1[tid][v_cnt_i], read_char[tid], op_dm_kl1[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr1[tid][v_cnt_i], read_char2[tid], op_dm_kr1[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if(n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if(n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if(s_r_o_l >= op_dm_kl1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", s_r_o_l + 1 - op_dm_kl1[tid][v_cnt_i]);
snt += sn;
}
if((s_r_o_l != -1) && (s_r_o_r != read_length))
{
if((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if(op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if(op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if(s_r_o_l == -1)
{
if(op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if(op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i]) ++nm_score;
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
}
if(read_length - s_r_o_r > op_dm_kr1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", read_length - s_r_o_r - op_dm_kr1[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
lv_re1f = nm_score;
if(n_cigar1) free(cigar1);
if(n_cigar2) free(cigar2);
#endif
}
else
{
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1);
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r);
#else
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid]);
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((op_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - op_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid]);
#endif
//deal with front and back lv cigar
m_m_n = s_r_o_r - s_r_o_l - 1;
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok (cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
if((s_r_o_l != -1) && (s_r_o_r != read_length))
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if(s_r_o_l == -1)
{
if(b_cigar[pchl] == 'M')
sn = sprintf(cigar_p1, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
else sn = sprintf(cigar_p1, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
else
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
}
sam_pos1 = sam_pos1 + i_n1 - d_n1;
}
if(op_rc[tid][v_cnt_i] == 0)
{
xa_d1s[tid][xa_i] = '+';
}
else
{
xa_d1s[tid][xa_i] = '-';
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos1s[tid][xa_i] = (uint32_t )sam_pos1 + s_offset1;
strcpy(cigar_p1s[tid][xa_i], cigar_p1);
lv_re1s[tid][xa_i] = lv_re1f;
xa_i++;
}
lv_re1f = dm_ops[tid];
#ifdef ALT_ALL
for(v_cnt_i = 0; (v_cnt_i < vs_cnt); v_cnt_i++)
#else
for(v_cnt_i = 0; (v_cnt_i < vs_cnt) && (v_cnt < 2) && (dm_op[tid] + 3 > dm_ops[tid]); v_cnt_i++)
#endif
{
x = ops_vector_pos1[tid][v_cnt_i];
low = 0;
high = chr_file_n - 1;
while ( low <= high )
{
mid = (low + high) >> 1;
if(x < (chr_end_n[mid]))
{
high = mid - 1;
}
else if(x > (chr_end_n[mid]))
{
low = mid + 1;
}
else
{
chr_re = mid;
break;
}
chr_re = low;
}
sam_pos1 = ops_vector_pos1[tid][v_cnt_i] - chr_end_n[chr_re - 1] + 1;
chr_res[tid][xa_i] = chr_re;
if(ops_rc[tid][v_cnt_i] == 0)
{
#ifdef CHAR_CP_SINGLE_END
read_bit_1[tid] = read_bit1[tid][0];
#else
strcpy(sam_seq1, seqio[seqi].read_seq1);
#endif
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][0];
qual_filt_lv_1_o = qual_filt_lv1[tid][1];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
{
mp_subs_1 = mp_subs1[tid][0];
mp_subs_1_o = mp_subs1[tid][1];
}
#endif
}
else
{
#ifdef CHAR_CP_SINGLE_END
read_bit_1[tid] = read_bit1[tid][1];
#else
for(sam_seq_i = 0; sam_seq_i < read_length; sam_seq_i++)
sam_seq1[sam_seq_i] = Dna5Tochar[charToDna5n[seqio[seqi].read_seq1[sam_seq_i]] ^ 0X3];
sam_seq1[sam_seq_i] = '\0';
strrev1(sam_seq1);
#endif
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
qual_filt_lv_1 = qual_filt_lv1[tid][1];
qual_filt_lv_1_o = qual_filt_lv1[tid][0];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
{
mp_subs_1 = mp_subs1[tid][1];
mp_subs_1_o = mp_subs1[tid][0];
}
#endif
}
d_n1 = 0;
i_n1 = 0;
s_offset1 = 0;
s_r_o_l = ops_dm_l1[tid][v_cnt_i];
s_r_o_r = ops_dm_r1[tid][v_cnt_i];
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] = 0;
#endif
if(s_r_o_l && (s_r_o_r == 0))
{
strcpy(cigar_p1, cigar_m[tid]);
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
{
for (bit_char_i = 0, read_b_i = 32; bit_char_i < read_length; bit_char_i++, read_b_i++)
if(((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3) != ((ops_vector_seq1[tid][v_cnt_i][read_b_i >> 5] >> ((31 - (read_b_i & 0X1f)) << 1)) & 0X3))
{
sub_t[tid] += mp_subs_1[bit_char_i];
}
}
#endif
}
else //indel
{
if((cir_n == cir_fix_n) && (local_ksw))
{
#ifdef KSW_ALN
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i >= 0
read_char[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; read_b_i < ops_dm_kl1[tid][v_cnt_i]; bit_char_i--, read_b_i++)//bit_char_i > -1
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(ops_dm_kl1[tid][v_cnt_i], read_char[tid], ops_dm_kl1[tid][v_cnt_i], ali_ref_seq[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar1, &cigar1);
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < ops_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length
read_char2[tid][read_b_i] = charToDna5n[sam_seq1[bit_char_i]];
#endif
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; read_b_i < op_dm_kr1[tid][v_cnt_i]; bit_char_i++, read_b_i++)//bit_char_i < read_length + 64
ali_ref_seq2[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
ksw_global(op_dm_kr1[tid][v_cnt_i], read_char2[tid], op_dm_kr1[tid][v_cnt_i], ali_ref_seq2[tid], 5, mat, gapo_score, gape_score, band_with, &n_cigar2, &cigar2);
m_m_n = s_r_o_r - s_r_o_l - 1;
nm_score = 0;
snt = 0;
if(n_cigar1)
{
op_score1 = cigar1[0]&0xf;
len_score1 = cigar1[0]>>4;
}
else op_score1 = 3;
if(n_cigar2)
{
op_score2 = cigar2[0]&0xf;
len_score2 = cigar2[0]>>4;
}
else op_score2 = 3;
if(s_r_o_l >= ops_dm_kl1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", s_r_o_l + 1 - ops_dm_kl1[tid][v_cnt_i]);
snt += sn;
}
if((s_r_o_l != -1) && (s_r_o_r != read_length))
{
if((op_score1 == 0) && (op_score2 == 0))
{
k_start1 = 0;
k_start2 = 1;
k_middle = len_score1 + len_score2 + m_m_n;
}
else if(op_score1 == 0)
{
k_start1 = 0;
k_start2 = 0;
k_middle = len_score1 + m_m_n;
}
else if(op_score2 == 0)
{
k_start1 = -1;
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start1 = -1;
k_start2 = 0;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1_o[read_length + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else if(s_r_o_l == -1)
{
if(op_score2 == 0)
{
k_start2 = 1;
k_middle = len_score2 + m_m_n;
}
else
{
k_start2 = 0;
k_middle = m_m_n;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
x_score = y_score = 0;
for (bit_char_i = k_start2; bit_char_i < n_cigar2; bit_char_i++)
{
op_score = cigar2[bit_char_i]&0xf;
len_score = cigar2[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char2[tid][x_score + read_b_i] != ali_ref_seq2[tid][y_score + read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1[s_r_o_r + x_score + read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score;
}
}
else
{
if(op_score1 == 0)
{
k_start1 = 0;
k_middle = len_score1 + m_m_n;
}
else
{
k_start1 = -1;
k_middle = m_m_n;
}
x_score = y_score = 0;
for (bit_char_i = n_cigar1 - 1; bit_char_i > k_start1; bit_char_i--)
{
op_score = cigar1[bit_char_i]&0xf;
len_score = cigar1[bit_char_i]>>4;
sn = sprintf(cigar_p1 + snt, "%d%c", len_score, ksw_cigars[op_score]);
snt += sn;
if (op_score == 0) // match
{
for (read_b_i = 0; read_b_i < len_score; ++read_b_i)
if (read_char[tid][n_cigar1 - 1 - x_score - read_b_i] != ali_ref_seq[tid][n_cigar1 - 1 - y_score - read_b_i])
{
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0)) sub_t[tid] += mp_subs_1_o[read_length + n_cigar1 - s_r_o_l - 2 - x_score - read_b_i];
#endif
++nm_score;
}
x_score += len_score;
y_score += len_score;
}
else if (op_score == 1) x_score += len_score, nm_score += len_score, i_n1 += len_score;
else if (op_score == 2) y_score += len_score, nm_score += len_score, d_n1 += len_score;
}
sn = sprintf(cigar_p1 + snt, "%dM", k_middle);
snt += sn;
}
if(read_length - s_r_o_r > ops_dm_kr1[tid][v_cnt_i])
{
sn = sprintf(cigar_p1 + snt, "%dS", read_length - s_r_o_r - ops_dm_kr1[tid][v_cnt_i]);
snt += sn;
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
lv_re1f = nm_score;
if(n_cigar1) free(cigar1);
if(n_cigar2) free(cigar2);
#endif
}
else
{
#ifdef QUAL_FILT_LV_OUT_SINGLE_END
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
computeEditDistanceWithCigar_s_mis_left_mp(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1, mp_subs_1_o + read_length - 1 - s_r_o_l, &(sub_t[tid]));
else computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1);
#else
computeEditDistanceWithCigar_s_mis_left(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], qual_filt_lv_1_o + read_length - 1 - s_r_o_l, &s_offset1);
#endif
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
computeEditDistanceWithCigar_s_mis_mp(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - ops_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r, mp_subs_1 + s_r_o_r, &(sub_t[tid]));
else computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - ops_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r);
#else
computeEditDistanceWithCigar_s_mis(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - ops_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], qual_filt_lv_1 + s_r_o_r);
#endif
#else
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > - 1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_l, read_b_i = 0; bit_char_i >= 0; bit_char_i--, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_l, read_b_i = 0; bit_char_i > -1; bit_char_i--, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid], mp_subs_1_o + read_length - 1 - s_r_o_l, &(sub_t[tid]));
else computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid]);
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 33 + s_r_o_l, read_char[tid], s_r_o_l + 1, lv_k, cigarBuf1, f_cigarn, L[tid]);
#endif
#ifdef CHAR_CP_SINGLE_END
for (bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = ((read_bit_1[tid][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
for (bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = ((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3);
#else
for(bit_char_i = s_r_o_r, read_b_i = 0; bit_char_i < read_length; bit_char_i++, read_b_i++)
read_char[tid][read_b_i] = sam_seq1[bit_char_i];
for(bit_char_i = 32 + s_r_o_r, read_b_i = 0; bit_char_i < read_length + 64; bit_char_i++, read_b_i++)
ali_ref_seq[tid][read_b_i] = Dna5Tochar[((ops_vector_seq1[tid][v_cnt_i][bit_char_i >> 5] >> ((31 - (bit_char_i & 0X1f)) << 1)) & 0X3)];
#endif
#ifdef MAPPING_QUALITY_SINGLE_END
if((mp_flag) && (v_cnt_i == 0))
computeEditDistanceWithCigar_s_mp(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - ops_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid], mp_subs_1 + s_r_o_r, &(sub_t[tid]));
else computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - ops_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid]);
#else
computeEditDistanceWithCigar_s(ali_ref_seq[tid], 32 + read_length - s_r_o_r, read_char[tid], read_length - ops_dm_r1[tid][v_cnt_i], lv_k, cigarBuf2, f_cigarn, L[tid]);
#endif
#endif
//deal with front and back lv cigar
m_m_n = s_r_o_r - s_r_o_l - 1;
strncpy(str_o, cigarBuf1, f_cigarn);
s_o = 0;
f_c = 0;
pch = strtok_r(cigarBuf1,"DMIS", &saveptr);
while (pch != NULL)
{
pchl = strlen(pch);
f_cigar[f_cigarn - f_c - 2] = atoi(pch);
s_o += (pchl + 1);
f_cigar[f_cigarn - f_c - 1] = str_o[s_o - 1];
f_c += 2;
if(str_o[s_o - 1] == 'D') d_n1 += atoi(pch);
if(str_o[s_o - 1] == 'I') i_n1 += atoi(pch);
pch = strtok_r(NULL, "DMIS", &saveptr);
}
strncpy(b_cigar, cigarBuf2, f_cigarn);
pch = strtok (cigarBuf2,"DMIS");
if(pch != NULL)
pchl = strlen(pch);
snt = 0;
if((s_r_o_l != -1) && (s_r_o_r != read_length))
{
if((f_cigar[f_cigarn - 1] == 'M') && (b_cigar[pchl] == 'M'))
{
f_cigar[f_cigarn - 2] += (m_m_n + atoi(pch));
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s", b_cigar + pchl + 1);
snt += sn;
}
else if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%s",b_cigar);
snt += sn;
}
else if(b_cigar[pchl] == 'M')
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
snt += sn;
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
}
else if(s_r_o_l == -1)
{
if(b_cigar[pchl] == 'M')
sn = sprintf(cigar_p1, "%uM%s", m_m_n + atoi(pch), b_cigar + pchl + 1);
else sn = sprintf(cigar_p1, "%uM%s", m_m_n, b_cigar);
snt += sn;
}
else
{
if(f_cigar[f_cigarn - 1] == 'M')
{
f_cigar[f_cigarn - 2] += m_m_n;
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
}
else
{
for(f_i = 0; f_i < f_c; f_i += 2)
{
sn = sprintf(cigar_p1 + snt, "%u%c", f_cigar[f_cigarn - f_c + f_i], f_cigar[f_cigarn + 1 - f_c + f_i]);
snt += sn;
}
sn = sprintf(cigar_p1 + snt, "%uM", m_m_n);
snt += sn;
}
}
//sn = sprintf(cigar_p1 + snt, "\0");
//snt += sn;
}
sam_pos1 = sam_pos1 + i_n1 - d_n1;
}
if(ops_rc[tid][v_cnt_i] == 0)
{
xa_d1s[tid][xa_i] = '+';
}
else
{
xa_d1s[tid][xa_i] = '-';
}
#ifdef NO_S_OFF
s_offset1 = 0;
#endif
sam_pos1s[tid][xa_i] = (uint32_t )sam_pos1 + s_offset1;
strcpy(cigar_p1s[tid][xa_i], cigar_p1);
lv_re1s[tid][xa_i] = lv_re1f;
xa_i++;
}
seqio[seqi].v_cnt = v_cnt;
if(v_cnt > 0)
{
#ifdef MAPPING_QUALITY
if(mp_flag)
{
if(xa_i)
{
log_tmp = log(vs_cnt);
sam_qual1 = (sam_qual1 - sub_t[tid] - log_tmp) * 3.434;
sam_qual1 = (sam_qual1 > 2 ? sam_qual1 : 2);
#ifdef QUAL_20
sam_qual1 = (sam_qual1 < 20 ? 20 : sam_qual1);
#endif
sam_qual1 = (sam_qual1 > 60 ? 60 : sam_qual1);
}
else
{
sam_qual1 = 60;
}
}
#endif
seqio[seqi].qualc1 = sam_qual1;
seqio[seqi].xa_n = xa_i;
if(xa_i > 0)
{
memcpy(chr_res_buffer[seqi], chr_res[tid], xa_i << 2);
seqio[seqi].chr_res = chr_res_buffer[seqi];
memcpy(xa_d1s_buffer[seqi], xa_d1s[tid], xa_i);
seqio[seqi].xa_d1s = xa_d1s_buffer[seqi];
memcpy(sam_pos1s_buffer[seqi], sam_pos1s[tid], xa_i << 2);
seqio[seqi].sam_pos1s = sam_pos1s_buffer[seqi];
memcpy(lv_re1s_buffer[seqi], lv_re1s[tid], xa_i << 2);
seqio[seqi].lv_re1s = lv_re1s_buffer[seqi];
for(v_cnt_i = 0; v_cnt_i < xa_i; v_cnt_i++)
{
pos_l = strlen(cigar_p1s[tid][v_cnt_i]) + 1;
if((seqio[seqi].cigar_p1s[v_cnt_i] = (char* )calloc(pos_l, 1)) == NULL) exit(1);//
memcpy(seqio[seqi].cigar_p1s[v_cnt_i], cigar_p1s[tid][v_cnt_i], pos_l - 1);
}
}
}
else
{
#ifdef OUTPUT_ARR
seqio[seqi].xa_n = 0;
seqio[seqi].flag1 = 4;
seqio[seqi].chr_re = chr_file_n;
seqio[seqi].pos1 = 0;
seqio[seqi].qualc1 = 0;
strcpy(pr_cigar1_buffer[seqi], "*");
seqio[seqi].cigar1 = pr_cigar1_buffer[seqi];
seqio[seqi].seq1 = seqio[seqi].read_seq1;
#endif
}
}
}
|
wokalski/Distraction-Free-Xcode-plugin | Archived/v1/WCDistractionFreeXcodePlugin/Headers/Frameworks/IDEKit/IDETemplateSection.h | <gh_stars>10-100
//
// Generated by class-dump 3.5 (64 bit).
//
// class-dump is Copyright (C) 1997-1998, 2000-2001, 2004-2013 by <NAME>.
//
#import "NSObject.h"
#import "IDEKeyDrivenNavigableItemRepresentedObject.h"
@class DVTDocumentLocation, DVTFileDataType, DVTPlatform, IDEFileReference, NSArray, NSImage, NSMutableDictionary, NSString;
@interface IDETemplateSection : NSObject <IDEKeyDrivenNavigableItemRepresentedObject>
{
NSMutableDictionary *_templateCategoriesByName;
NSArray *_categories;
DVTPlatform *_platform;
}
+ (id)keyPathsForValuesAffectingWillChangeDeviceSoftwareVersion;
@property(retain) DVTPlatform *platform; // @synthesize platform=_platform;
- (void).cxx_destruct;
@property(readonly) BOOL navigableItem_isMajorGroup;
@property(readonly) NSImage *navigableItem_image;
@property(readonly) NSString *navigableItem_name;
@property(readonly) NSArray *templates;
@property(readonly) NSArray *categories; // @synthesize categories=_categories;
- (void)sortAllCategories;
- (void)addTemplate:(id)arg1;
- (id)categoryWithName:(id)arg1;
@property(readonly) NSString *sectionIdentifier;
- (id)init;
// Remaining properties
@property(readonly, copy) NSString *debugDescription;
@property(readonly, copy) NSString *description;
@property(readonly) unsigned long long hash;
@property(readonly) DVTDocumentLocation *navigableItem_contentDocumentLocation;
@property(readonly) DVTFileDataType *navigableItem_documentType;
@property(readonly) IDEFileReference *navigableItem_fileReference;
@property(readonly) NSString *navigableItem_groupIdentifier;
@property(readonly) BOOL navigableItem_isLeaf;
@property(readonly) NSString *navigableItem_toolTip;
@property(readonly) Class superclass;
@end
|
openharmony-sig-ci/appexecfwk_standard | services/bundlemgr/include/ipc/installd_interface.h | <filename>services/bundlemgr/include/ipc/installd_interface.h<gh_stars>1-10
/*
* Copyright (c) 2021 Huawei Device Co., Ltd.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#ifndef FOUNDATION_APPEXECFWK_SERVICES_BUNDLEMGR_INCLUDE_IPC_INSTALLD_INTERFACE_H
#define FOUNDATION_APPEXECFWK_SERVICES_BUNDLEMGR_INCLUDE_IPC_INSTALLD_INTERFACE_H
#include <string>
#include <vector>
#include "iremote_broker.h"
#include "appexecfwk_errors.h"
namespace OHOS {
namespace AppExecFwk {
class IInstalld : public IRemoteBroker {
public:
DECLARE_INTERFACE_DESCRIPTOR(u"ohos.appexecfwk.Installd");
/**
* @brief Create a bundle code directory.
* @param bundleDir Indicates the bundle code directory path that to be created.
* @return Returns ERR_OK if the bundle directory created successfully; returns error code otherwise.
*/
virtual ErrCode CreateBundleDir(const std::string &bundleDir) = 0;
/**
* @brief Remove a bundle code directory.
* @param bundleDir Indicates the bundle code directory path that to be removed.
* @return Returns ERR_OK if the bundle directory removed successfully; returns error code otherwise.
*/
virtual ErrCode RemoveBundleDir(const std::string &bundleDir) = 0;
/**
* @brief Extract the files of a HAP module to the code directory.
* @param srcModulePath Indicates the HAP file path.
* @param targetPath Indicates the code directory path that the HAP to be extracted to.
* @return Returns ERR_OK if the HAP file extracted successfully; returns error code otherwise.
*/
virtual ErrCode ExtractModuleFiles(const std::string &srcModulePath, const std::string &destPath) = 0;
/**
* @brief Remove the module directory.
* @param moduleDir Indicates the module directory to be removed.
* @return Returns ERR_OK if the module directory removed successfully; returns error code otherwise.
*/
virtual ErrCode RemoveModuleDir(const std::string &moduleDir) = 0;
/**
* @brief Rename the module directory from temporaily path to the real path.
* @param oldPath Indicates the old path name.
* @param newPath Indicates the new path name.
* @return Returns ERR_OK if the module directory renamed successfully; returns error code otherwise.
*/
virtual ErrCode RenameModuleDir(const std::string &oldDir, const std::string &newDir) = 0;
/**
* @brief Create a bundle data directory.
* @param bundleDir Indicates the bundle data directory path that to be created.
* @param uid Indicates uid to be set to the directory.
* @param gid Indicates gid to be set to the directory.
* @return Returns ERR_OK if the bundle data directory created successfully; returns error code otherwise.
*/
virtual ErrCode CreateBundleDataDir(const std::string &bundleDir, const int uid, const int gid) = 0;
/**
* @brief Remove a bundle data directory.
* @param bundleDir Indicates the bundle data directory path that to be removed.
* @return Returns ERR_OK if the bundle data directory removed successfully; returns error code otherwise.
*/
virtual ErrCode RemoveBundleDataDir(const std::string &bundleDataDir) = 0;
/**
* @brief Create a module and it's abilities data directory.
* @param bundleDir Indicates the module data directory path that to be created.
* @param abilityDirs Indicates the abilities data directory name that to be created.
* @param uid Indicates uid to be set to the directory.
* @param gid Indicates gid to be set to the directory.
* @return Returns ERR_OK if the data directories created successfully; returns error code otherwise.
*/
virtual ErrCode CreateModuleDataDir(
const std::string &ModuleDir, const std::vector<std::string> &abilityDirs, const int uid, const int gid) = 0;
/**
* @brief Remove a module data directory.
* @param bundleDir Indicates the module data directory path that to be removed.
* @return Returns ERR_OK if the module data directory removed successfully; returns error code otherwise.
*/
virtual ErrCode RemoveModuleDataDir(const std::string &moduleDataDir) = 0;
/**
* @brief Clean all files in a bundle data directory.
* @param bundleDir Indicates the data directory path that to be cleaned.
* @return Returns ERR_OK if the data directory cleaned successfully; returns error code otherwise.
*/
virtual ErrCode CleanBundleDataDir(const std::string &bundleDir) = 0;
enum class Message {
CREATE_BUNDLE_DIR = 1,
REMOVE_BUNDLE_DIR,
EXTRACT_MODULE_FILES,
REMOVE_MODULE_DIR,
RENAME_MODULE_DIR,
CREATE_BUNDLE_DATA_DIR,
REMOVE_BUNDLE_DATA_DIR,
CREATE_MODULE_DATA_DIR,
REMOVE_MODULE_DATA_DIR,
CLEAN_BUNDLE_DATA_DIR,
};
};
} // namespace AppExecFwk
} // namespace OHOS
#endif // FOUNDATION_APPEXECFWK_SERVICES_BUNDLEMGR_INCLUDE_IPC_INSTALLD_INTERFACE_H |
chrisuehlinger/portfolio-gatsby | src/components/homepage/Talks.js | import React from 'react'
import { StaticQuery, graphql } from "gatsby"
import HomepageWaypoint from './parts/HomepageWaypoint';
import ShowCard from './parts/ShowCard';
import './talks.scss'
const Talks = () => (
<HomepageWaypoint zone="TALKS">
<div className="talks-page" id="talks">
<h2>Talks</h2>
<StaticQuery
query={graphql`
query TalkQuery {
allTalksYaml {
nodes {
company
description
id
title
url
clips {
height
id
src
type
width
image {
childImageSharp {
fluid(maxWidth: 300) {
...GatsbyImageSharpFluid
}
}
}
}
}
}
}
`}
render={data => data.allTalksYaml.nodes.map(talk => <ShowCard key={talk.id} {...talk}/>) }/>
</div>
</HomepageWaypoint>
);
export default Talks
|
shantyps/openosrs-dev | runelite-api/src/main/java/net/runelite/api/events/NameChangeEvent.java | <gh_stars>1-10
package net.runelite.api.events;
import lombok.Data;
import net.runelite.api.Actor;
/**
* @author Kris | 07/01/2022
*/
@Data
public class NameChangeEvent {
private final Actor actor;
private final String oldName;
private final String newName;
}
|
askmohanty/metasfresh | misc/services/mobile-webui/mobile-webui-frontend/src/reducers/wfProcesses_status/confirmation.js | <gh_stars>0
import * as types from '../../constants/UserConfirmationTypes';
import * as CompleteStatus from '../../constants/CompleteStatus';
import { updateUserEditable } from './utils';
import { registerHandler } from './activityStateHandlers';
const COMPONENT_TYPE = 'common/confirmButton';
export const activityUserConfirmationReducer = ({ draftState, action }) => {
switch (action.type) {
case types.SET_ACTIVITY_USER_CONFIRMED: {
console.log('SET_ACTIVITY_USER_CONFIRMED: ', action);
const { wfProcessId, activityId } = action.payload;
const draftWFProcess = draftState[wfProcessId];
const draftActivity = draftWFProcess.activities[activityId];
draftActivity.dataStored.confirmed = true;
draftActivity.dataStored.completeStatus = computeActivityStatus({
confirmed: draftActivity.dataStored.confirmed,
});
updateUserEditable({ draftWFProcess });
return draftState;
}
default: {
return draftState;
}
}
};
const computeActivityStatus = ({ confirmed }) => {
return confirmed ? CompleteStatus.COMPLETED : CompleteStatus.NOT_STARTED;
};
registerHandler({
componentType: COMPONENT_TYPE,
computeActivityDataStoredInitialValue: ({ componentProps }) => {
const confirmed = !!componentProps.confirmed;
return { confirmed: confirmed, completeStatus: computeActivityStatus({ confirmed }) };
},
});
|
npillmayer/gotype | engine/khipu/linebreak/firstfit/firstfit_test.go | <reponame>npillmayer/gotype<gh_stars>1-10
package firstfit
import (
"bytes"
"io"
"io/ioutil"
"strings"
"testing"
"github.com/npillmayer/gotype/core/config/gtrace"
"github.com/npillmayer/gotype/core/config/tracing"
"github.com/npillmayer/gotype/core/config/tracing/gotestingadapter"
"github.com/npillmayer/gotype/core/dimen"
"github.com/npillmayer/gotype/core/parameters"
"github.com/npillmayer/gotype/engine/khipu"
"github.com/npillmayer/gotype/engine/khipu/linebreak"
)
var graphviz = false // global switch for GraphViz DOT output
func TestBuffer(t *testing.T) {
//gtrace.CoreTracer = gologadapter.New()
gtrace.CoreTracer = gotestingadapter.New()
teardown := gotestingadapter.RedirectTracing(t)
defer teardown()
lb, _ := newTestLinebreaker(t, "Hello World!", 20)
k, ok := lb.peek()
if !ok || k.Type() != khipu.KTTextBox {
//t.Logf("lb.pos=%d, lb.mark=%d", lb.pos, lb.check)
t.Logf("lb.pos=%d", lb.pos)
t.Errorf("expected the first knot to be TextBox('Hello'), is %v", k)
}
if knot := lb.next(); k != knot {
t.Errorf("first knot is %v, re-read knot is %v", k, knot)
}
}
func TestBacktrack(t *testing.T) {
//gtrace.CoreTracer = gologadapter.New()
gtrace.CoreTracer = gotestingadapter.New()
teardown := gotestingadapter.RedirectTracing(t)
defer teardown()
lb, _ := newTestLinebreaker(t, "the quick brown fox jumps over the lazy dog.", 30)
k := lb.next()
lb.checkpoint()
lb.next()
lb.next()
lb.next()
knot := lb.backtrack()
if k != knot {
t.Errorf("remembered start knot is %v, backtracked knot is %v", k, knot)
}
k = lb.next()
lb.checkpoint()
knot = lb.backtrack()
if k != knot {
t.Errorf("remembered knot is %v, backtracked knot is %v", k, knot)
}
}
func TestLinebreak(t *testing.T) {
// gtrace.CoreTracer = gologadapter.New()
gtrace.CoreTracer = gotestingadapter.New()
teardown := gotestingadapter.RedirectTracing(t)
defer teardown()
lb, kh := newTestLinebreaker(t, "the quick brown fox jumps over the lazy dog.", 30)
breakpoints, err := lb.FindBreakpoints()
if err != nil {
t.Errorf(err.Error())
}
if len(breakpoints)-1 != 2 {
t.Errorf("exptected 'princess' to occupy 2 lines, got %d", len(breakpoints)-1)
}
t.Logf("# Paragraph with %d lines: %v", len(breakpoints)-1, breakpoints)
t.Logf(" |---------+---------+---------+|")
j := 0
for i := 1; i < len(breakpoints); i++ {
// t.Logf("%3d: %s", i, kh.Text(j, breakpoints[i].Position()))
text := kh.Text(j, breakpoints[i].Position())
t.Logf("%3d: %-30s|", i, justify(text, 30, i%2 == 0))
j = breakpoints[i].Position()
}
}
var princess = `In olden times when wishing still helped one, there lived a king whose daughters were all beautiful; and the youngest was so beautiful that the sun itself, which has seen so much, was astonished whenever it shone in her face. Close by the king's castle lay a great dark forest, and under an old lime-tree in the forest was a well, and when the day was very warm, the king's child went out into the forest and sat down by the side of the cool fountain; and when she was bored she took a golden ball, and threw it up on high and caught it; and this ball was her favorite plaything.`
func TestPrincess(t *testing.T) {
// gtrace.CoreTracer = gologadapter.New()
gtrace.CoreTracer = gotestingadapter.New()
teardown := gotestingadapter.RedirectTracing(t)
defer teardown()
lb, kh := newTestLinebreaker(t, princess, 45)
kh.AppendKnot(khipu.Penalty(-10000)) // TODO: add parfillskip
breakpoints, err := lb.FindBreakpoints()
if err != nil {
t.Errorf(err.Error())
}
if len(breakpoints)-1 != 14 {
t.Errorf("exptected 'princess' to occupy 14 lines, got %d", len(breakpoints)-1)
}
t.Logf("# Paragraph with %d lines: %v", len(breakpoints)-1, breakpoints)
t.Logf(" |---------+---------+---------+---------+-----|")
j := 0
for i := 1; i < len(breakpoints); i++ {
// t.Logf("%3d: %s", i, kh.Text(j, breakpoints[i].Position()))
text := kh.Text(j, breakpoints[i].Position())
t.Logf("%3d: %-45s|", i, justify(text, 45, i%2 == 0))
j = breakpoints[i].Position()
}
}
// --- Helpers ----------------------------------------------------------
func newTestLinebreaker(t *testing.T, text string, len int) (*linebreaker, *khipu.Khipu) {
kh, cursor, _ := setupFFTest(t, text, false)
parshape := linebreak.RectangularParShape(dimen.Dimen(len) * 10 * dimen.BP)
lb, err := newLinebreaker(cursor, parshape, nil)
if err != nil {
t.Error(err)
}
return lb, kh
}
func setupFFTest(t *testing.T, paragraph string, hyphens bool) (*khipu.Khipu, linebreak.Cursor, io.Writer) {
gtrace.CoreTracer.SetTraceLevel(tracing.LevelError)
regs := parameters.NewTypesettingRegisters()
if hyphens {
regs.Push(parameters.P_MINHYPHENLENGTH, 3) // allow hyphenation
} else {
regs.Push(parameters.P_MINHYPHENLENGTH, 100) // inhibit hyphenation
}
kh := khipu.KnotEncode(strings.NewReader(paragraph), nil, regs)
if kh == nil {
t.Errorf("no Khipu to test; input is %s", paragraph)
}
//kh.AppendKnot(khipu.Penalty(linebreak.InfinityMerits))
cursor := linebreak.NewFixedWidthCursor(khipu.NewCursor(kh), 10*dimen.BP, 0)
var dotfile io.Writer
var err error
if graphviz {
dotfile, err = ioutil.TempFile(".", "knuthplass-*.dot")
if err != nil {
t.Errorf(err.Error())
}
}
gtrace.CoreTracer.SetTraceLevel(tracing.LevelDebug)
return kh, cursor, dotfile
}
// -------------------------------------------------------------
// crude implementation just for testing
func justify(text string, l int, even bool) string {
t := strings.Trim(text, " \t\n")
d := l - len(t)
if d == 0 {
return t // fit
} else if d < 0 { // overfull box
return text + "\u25ae"
}
s := strings.Fields(text)
if len(s) == 1 {
return text
}
var b bytes.Buffer
W := 0 // length of all words
for _, w := range s {
W += len(w)
}
d = l - W // amount of WS to distribute
ws := d / (len(s) - 1)
r := d - ws*(len(s)-1) + 1
b.WriteString(s[0])
if even {
for j := 1; j < r; j++ {
for i := 0; i < ws+1; i++ {
b.WriteString(" ")
}
b.WriteString(s[j])
}
for j := r; j < len(s); j++ {
for i := 0; i < ws; i++ {
b.WriteString(" ")
}
b.WriteString(s[j])
}
} else {
for j := 1; j <= len(s)-r; j++ {
for i := 0; i < ws; i++ {
b.WriteString(" ")
}
b.WriteString(s[j])
}
for j := len(s) - r + 1; j < len(s); j++ {
for i := 0; i < ws+1; i++ {
b.WriteString(" ")
}
b.WriteString(s[j])
}
}
return b.String()
}
|
lishangwu/nodejs-mmall | src/dao/ShippingDao.js | <filename>src/dao/ShippingDao.js
import { Const } from '../common'
import { sequelize, Sequelize } from '../db/db'
const Op = Sequelize.Op
const model = require('../db/model')
const Shipping = model[Const.Entity.Shipping]
class ShippingDao {
async insert(shipping) {
return await Shipping.create(shipping)
}
async deleteByShippingIdUserId(userid, shippingId) {
return await Shipping.destroy({
where: {
user_id: userid,
id: shippingId
}
})
}
async updateByShipping(shipping){
return await Shipping.update(
shipping,
{
where: {id:shipping.id, user_id:shipping.user_id}
}
)
}
async selectByShippingIdUserId(userId,shippingId){
return await Shipping.findOne({
where: {
id: shippingId,
user_id: userId
}
})
}
async selectByUserId(userId){
return await Shipping.findAll({
where: {
user_id: userId
}
})
}
async selectByPrimaryKey(shipping_id){
return await Shipping.findOne({
where:{id: shipping_id}
})
}
}
module.exports = {
ShippingDao
} |
RobottDog/dcos-chronos | src/js/components/ConfigurationMapLabel.js | import React from "react";
const ConfigurationMapLabel = props => {
return (
<div className="configuration-map-label">
{props.children}
</div>
);
};
module.exports = ConfigurationMapLabel;
|
NicholsTyler/cse_335 | AquaLand/AquaLand/AquaLand/Fish.cpp | <gh_stars>0
/**
* \file Fish.cpp
*
* \author <NAME>
*/
#include "pch.h"
#include "Fish.h"
#include "Aquarium.h"
/// Maximum speed in the X direction in
/// in pixels per second
const double MaxSpeedX = 50;
/// Maximum speed in the Y direction in
/// in pixels per second
const double MaxSpeedY = 50;
/**
* Constructor
* \param aquarium The aquarium we are in
* \param filename Filename for the image we use
*/
CFish::CFish(CAquarium* aquarium, const std::wstring& filename) :
CItem(aquarium, filename)
{
mSpeedX = ((double)rand() / RAND_MAX) * MaxSpeedX;
mSpeedY = ((double)rand() / RAND_MAX) * MaxSpeedY;
}
/**
* Handle updates in time of our fish
*
* This is called before we draw and allows us to
* move our fish. We add our speed times the amount
* of time that has elapsed.
* \param elapsed Time elapsed since the class call
*/
void CFish::Update(double elapsed)
{
SetLocation(GetX() + mSpeedX * elapsed,
GetY() + mSpeedY * elapsed);
AdjustX();
AdjustY();
}
/**
* Handle needed x adjustments for fish
*
* This is called after updating fish location
* allowing for needed adjustments to image orientation
* and speed on the x axis.
*/
void CFish::AdjustX()
{
// X Location of fish + 10 pixels + half its width
double fishRight = GetX() + 10 + (GetItemWidth() / 2);
// X Location of fish - 10 pixels - half its width
double fishLeft = GetX() - 10 - (GetItemWidth() / 2);
if (mSpeedX > 0 && fishRight >= GetAquarium()->GetWidth())
{
mSpeedX = -mSpeedX;
SetMirror(mSpeedX < 0);
}
else if (mSpeedX < 0 && fishLeft <= 0)
{
mSpeedX = -mSpeedX;
SetMirror(mSpeedX < 0);
}
}
/**
* Handle needed y adjustments for fish
*
* This is called after updating fish location
* allowing for needed adjustments to speed on
* the y axis.
*/
void CFish::AdjustY()
{
// Y Location of fish + 10 pixels + half its height
double fishUp = GetY() + 10 + (GetItemHeight() / 2);
// Y Location of fish - 10 pixels - half its height
double fishDown = GetY() - 10 - (GetItemHeight() / 2);
if (mSpeedY > 0 && fishUp >= GetAquarium()->GetHeight())
{
mSpeedY = -mSpeedY;
}
else if (mSpeedY < 0 && fishDown <= 0)
{
mSpeedY = -mSpeedY;
}
}
/**
* Save this item to an XML node
* \param node The node we are going to be a child of
* \return the node we created
*/
std::shared_ptr<xmlnode::CXmlNode>
CFish::XmlSave(const std::shared_ptr<xmlnode::CXmlNode>& node)
{
auto itemNode = node->AddChild(L"item");
itemNode->SetAttribute(L"x", GetX());
itemNode->SetAttribute(L"y", GetY());
itemNode->SetAttribute(L"xSpeed", mSpeedX);
itemNode->SetAttribute(L"ySpeed", mSpeedY);
return itemNode;
}
/**
* Load the attributes for an item node.
*
* Override of the base class version. Adds attributes
* for x and y speed.
*
* \param node The Xml node we are loading the item from
*/
void CFish::XmlLoad(const std::shared_ptr<xmlnode::CXmlNode>& node)
{
CItem::XmlLoad(node);
mSpeedX = node->GetAttributeDoubleValue(L"xSpeed", 0);
mSpeedY = node->GetAttributeDoubleValue(L"ySpeed", 0);
} |
gedorinku/prolab-accounts | infra/record/entries.go | <filename>infra/record/entries.go
// Code generated by SQLBoiler (https://github.com/volatiletech/sqlboiler). DO NOT EDIT.
// This file is meant to be re-generated in place and/or deleted at any time.
package record
import (
"context"
"database/sql"
"fmt"
"reflect"
"strconv"
"strings"
"sync"
"time"
"github.com/pkg/errors"
"github.com/volatiletech/sqlboiler/boil"
"github.com/volatiletech/sqlboiler/queries"
"github.com/volatiletech/sqlboiler/queries/qm"
"github.com/volatiletech/sqlboiler/queries/qmhelper"
"github.com/volatiletech/sqlboiler/strmangle"
)
// Entry is an object representing the database table.
type Entry struct {
ID int64 `boil:"id" json:"id" toml:"id" yaml:"id"`
Title string `boil:"title" json:"title" toml:"title" yaml:"title"`
Description string `boil:"description" json:"description" toml:"description" yaml:"description"`
Content string `boil:"content" json:"content" toml:"content" yaml:"content"`
Link string `boil:"link" json:"link" toml:"link" yaml:"link"`
AuthorID int64 `boil:"author_id" json:"author_id" toml:"author_id" yaml:"author_id"`
GUID string `boil:"guid" json:"guid" toml:"guid" yaml:"guid"`
ImageURL string `boil:"image_url" json:"image_url" toml:"image_url" yaml:"image_url"`
BlogID int64 `boil:"blog_id" json:"blog_id" toml:"blog_id" yaml:"blog_id"`
PublishedAt time.Time `boil:"published_at" json:"published_at" toml:"published_at" yaml:"published_at"`
CreatedAt time.Time `boil:"created_at" json:"created_at" toml:"created_at" yaml:"created_at"`
UpdatedAt time.Time `boil:"updated_at" json:"updated_at" toml:"updated_at" yaml:"updated_at"`
R *entryR `boil:"-" json:"-" toml:"-" yaml:"-"`
L entryL `boil:"-" json:"-" toml:"-" yaml:"-"`
}
var EntryColumns = struct {
ID string
Title string
Description string
Content string
Link string
AuthorID string
GUID string
ImageURL string
BlogID string
PublishedAt string
CreatedAt string
UpdatedAt string
}{
ID: "id",
Title: "title",
Description: "description",
Content: "content",
Link: "link",
AuthorID: "author_id",
GUID: "guid",
ImageURL: "image_url",
BlogID: "blog_id",
PublishedAt: "published_at",
CreatedAt: "created_at",
UpdatedAt: "updated_at",
}
// Generated where
var EntryWhere = struct {
ID whereHelperint64
Title whereHelperstring
Description whereHelperstring
Content whereHelperstring
Link whereHelperstring
AuthorID whereHelperint64
GUID whereHelperstring
ImageURL whereHelperstring
BlogID whereHelperint64
PublishedAt whereHelpertime_Time
CreatedAt whereHelpertime_Time
UpdatedAt whereHelpertime_Time
}{
ID: whereHelperint64{field: `id`},
Title: whereHelperstring{field: `title`},
Description: whereHelperstring{field: `description`},
Content: whereHelperstring{field: `content`},
Link: whereHelperstring{field: `link`},
AuthorID: whereHelperint64{field: `author_id`},
GUID: whereHelperstring{field: `guid`},
ImageURL: whereHelperstring{field: `image_url`},
BlogID: whereHelperint64{field: `blog_id`},
PublishedAt: whereHelpertime_Time{field: `published_at`},
CreatedAt: whereHelpertime_Time{field: `created_at`},
UpdatedAt: whereHelpertime_Time{field: `updated_at`},
}
// EntryRels is where relationship names are stored.
var EntryRels = struct {
Author string
Blog string
}{
Author: "Author",
Blog: "Blog",
}
// entryR is where relationships are stored.
type entryR struct {
Author *User
Blog *Blog
}
// NewStruct creates a new relationship struct
func (*entryR) NewStruct() *entryR {
return &entryR{}
}
// entryL is where Load methods for each relationship are stored.
type entryL struct{}
var (
entryColumns = []string{"id", "title", "description", "content", "link", "author_id", "guid", "image_url", "blog_id", "published_at", "created_at", "updated_at"}
entryColumnsWithoutDefault = []string{"title", "description", "content", "link", "author_id", "guid", "image_url", "blog_id", "published_at", "created_at", "updated_at"}
entryColumnsWithDefault = []string{"id"}
entryPrimaryKeyColumns = []string{"id"}
)
type (
// EntrySlice is an alias for a slice of pointers to Entry.
// This should generally be used opposed to []Entry.
EntrySlice []*Entry
// EntryHook is the signature for custom Entry hook methods
EntryHook func(context.Context, boil.ContextExecutor, *Entry) error
entryQuery struct {
*queries.Query
}
)
// Cache for insert, update and upsert
var (
entryType = reflect.TypeOf(&Entry{})
entryMapping = queries.MakeStructMapping(entryType)
entryPrimaryKeyMapping, _ = queries.BindMapping(entryType, entryMapping, entryPrimaryKeyColumns)
entryInsertCacheMut sync.RWMutex
entryInsertCache = make(map[string]insertCache)
entryUpdateCacheMut sync.RWMutex
entryUpdateCache = make(map[string]updateCache)
entryUpsertCacheMut sync.RWMutex
entryUpsertCache = make(map[string]insertCache)
)
var (
// Force time package dependency for automated UpdatedAt/CreatedAt.
_ = time.Second
// Force qmhelper dependency for where clause generation (which doesn't
// always happen)
_ = qmhelper.Where
)
var entryBeforeInsertHooks []EntryHook
var entryBeforeUpdateHooks []EntryHook
var entryBeforeDeleteHooks []EntryHook
var entryBeforeUpsertHooks []EntryHook
var entryAfterInsertHooks []EntryHook
var entryAfterSelectHooks []EntryHook
var entryAfterUpdateHooks []EntryHook
var entryAfterDeleteHooks []EntryHook
var entryAfterUpsertHooks []EntryHook
// doBeforeInsertHooks executes all "before insert" hooks.
func (o *Entry) doBeforeInsertHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryBeforeInsertHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doBeforeUpdateHooks executes all "before Update" hooks.
func (o *Entry) doBeforeUpdateHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryBeforeUpdateHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doBeforeDeleteHooks executes all "before Delete" hooks.
func (o *Entry) doBeforeDeleteHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryBeforeDeleteHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doBeforeUpsertHooks executes all "before Upsert" hooks.
func (o *Entry) doBeforeUpsertHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryBeforeUpsertHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doAfterInsertHooks executes all "after Insert" hooks.
func (o *Entry) doAfterInsertHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryAfterInsertHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doAfterSelectHooks executes all "after Select" hooks.
func (o *Entry) doAfterSelectHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryAfterSelectHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doAfterUpdateHooks executes all "after Update" hooks.
func (o *Entry) doAfterUpdateHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryAfterUpdateHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doAfterDeleteHooks executes all "after Delete" hooks.
func (o *Entry) doAfterDeleteHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryAfterDeleteHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// doAfterUpsertHooks executes all "after Upsert" hooks.
func (o *Entry) doAfterUpsertHooks(ctx context.Context, exec boil.ContextExecutor) (err error) {
if boil.HooksAreSkipped(ctx) {
return nil
}
for _, hook := range entryAfterUpsertHooks {
if err := hook(ctx, exec, o); err != nil {
return err
}
}
return nil
}
// AddEntryHook registers your hook function for all future operations.
func AddEntryHook(hookPoint boil.HookPoint, entryHook EntryHook) {
switch hookPoint {
case boil.BeforeInsertHook:
entryBeforeInsertHooks = append(entryBeforeInsertHooks, entryHook)
case boil.BeforeUpdateHook:
entryBeforeUpdateHooks = append(entryBeforeUpdateHooks, entryHook)
case boil.BeforeDeleteHook:
entryBeforeDeleteHooks = append(entryBeforeDeleteHooks, entryHook)
case boil.BeforeUpsertHook:
entryBeforeUpsertHooks = append(entryBeforeUpsertHooks, entryHook)
case boil.AfterInsertHook:
entryAfterInsertHooks = append(entryAfterInsertHooks, entryHook)
case boil.AfterSelectHook:
entryAfterSelectHooks = append(entryAfterSelectHooks, entryHook)
case boil.AfterUpdateHook:
entryAfterUpdateHooks = append(entryAfterUpdateHooks, entryHook)
case boil.AfterDeleteHook:
entryAfterDeleteHooks = append(entryAfterDeleteHooks, entryHook)
case boil.AfterUpsertHook:
entryAfterUpsertHooks = append(entryAfterUpsertHooks, entryHook)
}
}
// One returns a single entry record from the query.
func (q entryQuery) One(ctx context.Context, exec boil.ContextExecutor) (*Entry, error) {
o := &Entry{}
queries.SetLimit(q.Query, 1)
err := q.Bind(ctx, exec, o)
if err != nil {
if errors.Cause(err) == sql.ErrNoRows {
return nil, sql.ErrNoRows
}
return nil, errors.Wrap(err, "record: failed to execute a one query for entries")
}
if err := o.doAfterSelectHooks(ctx, exec); err != nil {
return o, err
}
return o, nil
}
// All returns all Entry records from the query.
func (q entryQuery) All(ctx context.Context, exec boil.ContextExecutor) (EntrySlice, error) {
var o []*Entry
err := q.Bind(ctx, exec, &o)
if err != nil {
return nil, errors.Wrap(err, "record: failed to assign all query results to Entry slice")
}
if len(entryAfterSelectHooks) != 0 {
for _, obj := range o {
if err := obj.doAfterSelectHooks(ctx, exec); err != nil {
return o, err
}
}
}
return o, nil
}
// Count returns the count of all Entry records in the query.
func (q entryQuery) Count(ctx context.Context, exec boil.ContextExecutor) (int64, error) {
var count int64
queries.SetSelect(q.Query, nil)
queries.SetCount(q.Query)
err := q.Query.QueryRowContext(ctx, exec).Scan(&count)
if err != nil {
return 0, errors.Wrap(err, "record: failed to count entries rows")
}
return count, nil
}
// Exists checks if the row exists in the table.
func (q entryQuery) Exists(ctx context.Context, exec boil.ContextExecutor) (bool, error) {
var count int64
queries.SetSelect(q.Query, nil)
queries.SetCount(q.Query)
queries.SetLimit(q.Query, 1)
err := q.Query.QueryRowContext(ctx, exec).Scan(&count)
if err != nil {
return false, errors.Wrap(err, "record: failed to check if entries exists")
}
return count > 0, nil
}
// Author pointed to by the foreign key.
func (o *Entry) Author(mods ...qm.QueryMod) userQuery {
queryMods := []qm.QueryMod{
qm.Where("id=?", o.AuthorID),
}
queryMods = append(queryMods, mods...)
query := Users(queryMods...)
queries.SetFrom(query.Query, "\"users\"")
return query
}
// Blog pointed to by the foreign key.
func (o *Entry) Blog(mods ...qm.QueryMod) blogQuery {
queryMods := []qm.QueryMod{
qm.Where("id=?", o.BlogID),
}
queryMods = append(queryMods, mods...)
query := Blogs(queryMods...)
queries.SetFrom(query.Query, "\"blogs\"")
return query
}
// LoadAuthor allows an eager lookup of values, cached into the
// loaded structs of the objects. This is for an N-1 relationship.
func (entryL) LoadAuthor(ctx context.Context, e boil.ContextExecutor, singular bool, maybeEntry interface{}, mods queries.Applicator) error {
var slice []*Entry
var object *Entry
if singular {
object = maybeEntry.(*Entry)
} else {
slice = *maybeEntry.(*[]*Entry)
}
args := make([]interface{}, 0, 1)
if singular {
if object.R == nil {
object.R = &entryR{}
}
args = append(args, object.AuthorID)
} else {
Outer:
for _, obj := range slice {
if obj.R == nil {
obj.R = &entryR{}
}
for _, a := range args {
if a == obj.AuthorID {
continue Outer
}
}
args = append(args, obj.AuthorID)
}
}
if len(args) == 0 {
return nil
}
query := NewQuery(qm.From(`users`), qm.WhereIn(`id in ?`, args...))
if mods != nil {
mods.Apply(query)
}
results, err := query.QueryContext(ctx, e)
if err != nil {
return errors.Wrap(err, "failed to eager load User")
}
var resultSlice []*User
if err = queries.Bind(results, &resultSlice); err != nil {
return errors.Wrap(err, "failed to bind eager loaded slice User")
}
if err = results.Close(); err != nil {
return errors.Wrap(err, "failed to close results of eager load for users")
}
if err = results.Err(); err != nil {
return errors.Wrap(err, "error occurred during iteration of eager loaded relations for users")
}
if len(entryAfterSelectHooks) != 0 {
for _, obj := range resultSlice {
if err := obj.doAfterSelectHooks(ctx, e); err != nil {
return err
}
}
}
if len(resultSlice) == 0 {
return nil
}
if singular {
foreign := resultSlice[0]
object.R.Author = foreign
if foreign.R == nil {
foreign.R = &userR{}
}
foreign.R.AuthorEntries = append(foreign.R.AuthorEntries, object)
return nil
}
for _, local := range slice {
for _, foreign := range resultSlice {
if local.AuthorID == foreign.ID {
local.R.Author = foreign
if foreign.R == nil {
foreign.R = &userR{}
}
foreign.R.AuthorEntries = append(foreign.R.AuthorEntries, local)
break
}
}
}
return nil
}
// LoadBlog allows an eager lookup of values, cached into the
// loaded structs of the objects. This is for an N-1 relationship.
func (entryL) LoadBlog(ctx context.Context, e boil.ContextExecutor, singular bool, maybeEntry interface{}, mods queries.Applicator) error {
var slice []*Entry
var object *Entry
if singular {
object = maybeEntry.(*Entry)
} else {
slice = *maybeEntry.(*[]*Entry)
}
args := make([]interface{}, 0, 1)
if singular {
if object.R == nil {
object.R = &entryR{}
}
args = append(args, object.BlogID)
} else {
Outer:
for _, obj := range slice {
if obj.R == nil {
obj.R = &entryR{}
}
for _, a := range args {
if a == obj.BlogID {
continue Outer
}
}
args = append(args, obj.BlogID)
}
}
if len(args) == 0 {
return nil
}
query := NewQuery(qm.From(`blogs`), qm.WhereIn(`id in ?`, args...))
if mods != nil {
mods.Apply(query)
}
results, err := query.QueryContext(ctx, e)
if err != nil {
return errors.Wrap(err, "failed to eager load Blog")
}
var resultSlice []*Blog
if err = queries.Bind(results, &resultSlice); err != nil {
return errors.Wrap(err, "failed to bind eager loaded slice Blog")
}
if err = results.Close(); err != nil {
return errors.Wrap(err, "failed to close results of eager load for blogs")
}
if err = results.Err(); err != nil {
return errors.Wrap(err, "error occurred during iteration of eager loaded relations for blogs")
}
if len(entryAfterSelectHooks) != 0 {
for _, obj := range resultSlice {
if err := obj.doAfterSelectHooks(ctx, e); err != nil {
return err
}
}
}
if len(resultSlice) == 0 {
return nil
}
if singular {
foreign := resultSlice[0]
object.R.Blog = foreign
if foreign.R == nil {
foreign.R = &blogR{}
}
foreign.R.Entries = append(foreign.R.Entries, object)
return nil
}
for _, local := range slice {
for _, foreign := range resultSlice {
if local.BlogID == foreign.ID {
local.R.Blog = foreign
if foreign.R == nil {
foreign.R = &blogR{}
}
foreign.R.Entries = append(foreign.R.Entries, local)
break
}
}
}
return nil
}
// SetAuthor of the entry to the related item.
// Sets o.R.Author to related.
// Adds o to related.R.AuthorEntries.
func (o *Entry) SetAuthor(ctx context.Context, exec boil.ContextExecutor, insert bool, related *User) error {
var err error
if insert {
if err = related.Insert(ctx, exec, boil.Infer()); err != nil {
return errors.Wrap(err, "failed to insert into foreign table")
}
}
updateQuery := fmt.Sprintf(
"UPDATE \"entries\" SET %s WHERE %s",
strmangle.SetParamNames("\"", "\"", 1, []string{"author_id"}),
strmangle.WhereClause("\"", "\"", 2, entryPrimaryKeyColumns),
)
values := []interface{}{related.ID, o.ID}
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, updateQuery)
fmt.Fprintln(boil.DebugWriter, values)
}
if _, err = exec.ExecContext(ctx, updateQuery, values...); err != nil {
return errors.Wrap(err, "failed to update local table")
}
o.AuthorID = related.ID
if o.R == nil {
o.R = &entryR{
Author: related,
}
} else {
o.R.Author = related
}
if related.R == nil {
related.R = &userR{
AuthorEntries: EntrySlice{o},
}
} else {
related.R.AuthorEntries = append(related.R.AuthorEntries, o)
}
return nil
}
// SetBlog of the entry to the related item.
// Sets o.R.Blog to related.
// Adds o to related.R.Entries.
func (o *Entry) SetBlog(ctx context.Context, exec boil.ContextExecutor, insert bool, related *Blog) error {
var err error
if insert {
if err = related.Insert(ctx, exec, boil.Infer()); err != nil {
return errors.Wrap(err, "failed to insert into foreign table")
}
}
updateQuery := fmt.Sprintf(
"UPDATE \"entries\" SET %s WHERE %s",
strmangle.SetParamNames("\"", "\"", 1, []string{"blog_id"}),
strmangle.WhereClause("\"", "\"", 2, entryPrimaryKeyColumns),
)
values := []interface{}{related.ID, o.ID}
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, updateQuery)
fmt.Fprintln(boil.DebugWriter, values)
}
if _, err = exec.ExecContext(ctx, updateQuery, values...); err != nil {
return errors.Wrap(err, "failed to update local table")
}
o.BlogID = related.ID
if o.R == nil {
o.R = &entryR{
Blog: related,
}
} else {
o.R.Blog = related
}
if related.R == nil {
related.R = &blogR{
Entries: EntrySlice{o},
}
} else {
related.R.Entries = append(related.R.Entries, o)
}
return nil
}
// Entries retrieves all the records using an executor.
func Entries(mods ...qm.QueryMod) entryQuery {
mods = append(mods, qm.From("\"entries\""))
return entryQuery{NewQuery(mods...)}
}
// FindEntry retrieves a single record by ID with an executor.
// If selectCols is empty Find will return all columns.
func FindEntry(ctx context.Context, exec boil.ContextExecutor, iD int64, selectCols ...string) (*Entry, error) {
entryObj := &Entry{}
sel := "*"
if len(selectCols) > 0 {
sel = strings.Join(strmangle.IdentQuoteSlice(dialect.LQ, dialect.RQ, selectCols), ",")
}
query := fmt.Sprintf(
"select %s from \"entries\" where \"id\"=$1", sel,
)
q := queries.Raw(query, iD)
err := q.Bind(ctx, exec, entryObj)
if err != nil {
if errors.Cause(err) == sql.ErrNoRows {
return nil, sql.ErrNoRows
}
return nil, errors.Wrap(err, "record: unable to select from entries")
}
return entryObj, nil
}
// Insert a single record using an executor.
// See boil.Columns.InsertColumnSet documentation to understand column list inference for inserts.
func (o *Entry) Insert(ctx context.Context, exec boil.ContextExecutor, columns boil.Columns) error {
if o == nil {
return errors.New("record: no entries provided for insertion")
}
var err error
if !boil.TimestampsAreSkipped(ctx) {
currTime := time.Now().In(boil.GetLocation())
if o.CreatedAt.IsZero() {
o.CreatedAt = currTime
}
if o.UpdatedAt.IsZero() {
o.UpdatedAt = currTime
}
}
if err := o.doBeforeInsertHooks(ctx, exec); err != nil {
return err
}
nzDefaults := queries.NonZeroDefaultSet(entryColumnsWithDefault, o)
key := makeCacheKey(columns, nzDefaults)
entryInsertCacheMut.RLock()
cache, cached := entryInsertCache[key]
entryInsertCacheMut.RUnlock()
if !cached {
wl, returnColumns := columns.InsertColumnSet(
entryColumns,
entryColumnsWithDefault,
entryColumnsWithoutDefault,
nzDefaults,
)
cache.valueMapping, err = queries.BindMapping(entryType, entryMapping, wl)
if err != nil {
return err
}
cache.retMapping, err = queries.BindMapping(entryType, entryMapping, returnColumns)
if err != nil {
return err
}
if len(wl) != 0 {
cache.query = fmt.Sprintf("INSERT INTO \"entries\" (\"%s\") %%sVALUES (%s)%%s", strings.Join(wl, "\",\""), strmangle.Placeholders(dialect.UseIndexPlaceholders, len(wl), 1, 1))
} else {
cache.query = "INSERT INTO \"entries\" %sDEFAULT VALUES%s"
}
var queryOutput, queryReturning string
if len(cache.retMapping) != 0 {
queryReturning = fmt.Sprintf(" RETURNING \"%s\"", strings.Join(returnColumns, "\",\""))
}
cache.query = fmt.Sprintf(cache.query, queryOutput, queryReturning)
}
value := reflect.Indirect(reflect.ValueOf(o))
vals := queries.ValuesFromMapping(value, cache.valueMapping)
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, cache.query)
fmt.Fprintln(boil.DebugWriter, vals)
}
if len(cache.retMapping) != 0 {
err = exec.QueryRowContext(ctx, cache.query, vals...).Scan(queries.PtrsFromMapping(value, cache.retMapping)...)
} else {
_, err = exec.ExecContext(ctx, cache.query, vals...)
}
if err != nil {
return errors.Wrap(err, "record: unable to insert into entries")
}
if !cached {
entryInsertCacheMut.Lock()
entryInsertCache[key] = cache
entryInsertCacheMut.Unlock()
}
return o.doAfterInsertHooks(ctx, exec)
}
// Update uses an executor to update the Entry.
// See boil.Columns.UpdateColumnSet documentation to understand column list inference for updates.
// Update does not automatically update the record in case of default values. Use .Reload() to refresh the records.
func (o *Entry) Update(ctx context.Context, exec boil.ContextExecutor, columns boil.Columns) (int64, error) {
if !boil.TimestampsAreSkipped(ctx) {
currTime := time.Now().In(boil.GetLocation())
o.UpdatedAt = currTime
}
var err error
if err = o.doBeforeUpdateHooks(ctx, exec); err != nil {
return 0, err
}
key := makeCacheKey(columns, nil)
entryUpdateCacheMut.RLock()
cache, cached := entryUpdateCache[key]
entryUpdateCacheMut.RUnlock()
if !cached {
wl := columns.UpdateColumnSet(
entryColumns,
entryPrimaryKeyColumns,
)
if !columns.IsWhitelist() {
wl = strmangle.SetComplement(wl, []string{"created_at"})
}
if len(wl) == 0 {
return 0, errors.New("record: unable to update entries, could not build whitelist")
}
cache.query = fmt.Sprintf("UPDATE \"entries\" SET %s WHERE %s",
strmangle.SetParamNames("\"", "\"", 1, wl),
strmangle.WhereClause("\"", "\"", len(wl)+1, entryPrimaryKeyColumns),
)
cache.valueMapping, err = queries.BindMapping(entryType, entryMapping, append(wl, entryPrimaryKeyColumns...))
if err != nil {
return 0, err
}
}
values := queries.ValuesFromMapping(reflect.Indirect(reflect.ValueOf(o)), cache.valueMapping)
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, cache.query)
fmt.Fprintln(boil.DebugWriter, values)
}
var result sql.Result
result, err = exec.ExecContext(ctx, cache.query, values...)
if err != nil {
return 0, errors.Wrap(err, "record: unable to update entries row")
}
rowsAff, err := result.RowsAffected()
if err != nil {
return 0, errors.Wrap(err, "record: failed to get rows affected by update for entries")
}
if !cached {
entryUpdateCacheMut.Lock()
entryUpdateCache[key] = cache
entryUpdateCacheMut.Unlock()
}
return rowsAff, o.doAfterUpdateHooks(ctx, exec)
}
// UpdateAll updates all rows with the specified column values.
func (q entryQuery) UpdateAll(ctx context.Context, exec boil.ContextExecutor, cols M) (int64, error) {
queries.SetUpdate(q.Query, cols)
result, err := q.Query.ExecContext(ctx, exec)
if err != nil {
return 0, errors.Wrap(err, "record: unable to update all for entries")
}
rowsAff, err := result.RowsAffected()
if err != nil {
return 0, errors.Wrap(err, "record: unable to retrieve rows affected for entries")
}
return rowsAff, nil
}
// UpdateAll updates all rows with the specified column values, using an executor.
func (o EntrySlice) UpdateAll(ctx context.Context, exec boil.ContextExecutor, cols M) (int64, error) {
ln := int64(len(o))
if ln == 0 {
return 0, nil
}
if len(cols) == 0 {
return 0, errors.New("record: update all requires at least one column argument")
}
colNames := make([]string, len(cols))
args := make([]interface{}, len(cols))
i := 0
for name, value := range cols {
colNames[i] = name
args[i] = value
i++
}
// Append all of the primary key values for each column
for _, obj := range o {
pkeyArgs := queries.ValuesFromMapping(reflect.Indirect(reflect.ValueOf(obj)), entryPrimaryKeyMapping)
args = append(args, pkeyArgs...)
}
sql := fmt.Sprintf("UPDATE \"entries\" SET %s WHERE %s",
strmangle.SetParamNames("\"", "\"", 1, colNames),
strmangle.WhereClauseRepeated(string(dialect.LQ), string(dialect.RQ), len(colNames)+1, entryPrimaryKeyColumns, len(o)))
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, sql)
fmt.Fprintln(boil.DebugWriter, args...)
}
result, err := exec.ExecContext(ctx, sql, args...)
if err != nil {
return 0, errors.Wrap(err, "record: unable to update all in entry slice")
}
rowsAff, err := result.RowsAffected()
if err != nil {
return 0, errors.Wrap(err, "record: unable to retrieve rows affected all in update all entry")
}
return rowsAff, nil
}
// Upsert attempts an insert using an executor, and does an update or ignore on conflict.
// See boil.Columns documentation for how to properly use updateColumns and insertColumns.
func (o *Entry) Upsert(ctx context.Context, exec boil.ContextExecutor, updateOnConflict bool, conflictColumns []string, updateColumns, insertColumns boil.Columns) error {
if o == nil {
return errors.New("record: no entries provided for upsert")
}
if !boil.TimestampsAreSkipped(ctx) {
currTime := time.Now().In(boil.GetLocation())
if o.CreatedAt.IsZero() {
o.CreatedAt = currTime
}
o.UpdatedAt = currTime
}
if err := o.doBeforeUpsertHooks(ctx, exec); err != nil {
return err
}
nzDefaults := queries.NonZeroDefaultSet(entryColumnsWithDefault, o)
// Build cache key in-line uglily - mysql vs psql problems
buf := strmangle.GetBuffer()
if updateOnConflict {
buf.WriteByte('t')
} else {
buf.WriteByte('f')
}
buf.WriteByte('.')
for _, c := range conflictColumns {
buf.WriteString(c)
}
buf.WriteByte('.')
buf.WriteString(strconv.Itoa(updateColumns.Kind))
for _, c := range updateColumns.Cols {
buf.WriteString(c)
}
buf.WriteByte('.')
buf.WriteString(strconv.Itoa(insertColumns.Kind))
for _, c := range insertColumns.Cols {
buf.WriteString(c)
}
buf.WriteByte('.')
for _, c := range nzDefaults {
buf.WriteString(c)
}
key := buf.String()
strmangle.PutBuffer(buf)
entryUpsertCacheMut.RLock()
cache, cached := entryUpsertCache[key]
entryUpsertCacheMut.RUnlock()
var err error
if !cached {
insert, ret := insertColumns.InsertColumnSet(
entryColumns,
entryColumnsWithDefault,
entryColumnsWithoutDefault,
nzDefaults,
)
update := updateColumns.UpdateColumnSet(
entryColumns,
entryPrimaryKeyColumns,
)
if updateOnConflict && len(update) == 0 {
return errors.New("record: unable to upsert entries, could not build update column list")
}
conflict := conflictColumns
if len(conflict) == 0 {
conflict = make([]string, len(entryPrimaryKeyColumns))
copy(conflict, entryPrimaryKeyColumns)
}
cache.query = buildUpsertQueryPostgres(dialect, "\"entries\"", updateOnConflict, ret, update, conflict, insert)
cache.valueMapping, err = queries.BindMapping(entryType, entryMapping, insert)
if err != nil {
return err
}
if len(ret) != 0 {
cache.retMapping, err = queries.BindMapping(entryType, entryMapping, ret)
if err != nil {
return err
}
}
}
value := reflect.Indirect(reflect.ValueOf(o))
vals := queries.ValuesFromMapping(value, cache.valueMapping)
var returns []interface{}
if len(cache.retMapping) != 0 {
returns = queries.PtrsFromMapping(value, cache.retMapping)
}
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, cache.query)
fmt.Fprintln(boil.DebugWriter, vals)
}
if len(cache.retMapping) != 0 {
err = exec.QueryRowContext(ctx, cache.query, vals...).Scan(returns...)
if err == sql.ErrNoRows {
err = nil // Postgres doesn't return anything when there's no update
}
} else {
_, err = exec.ExecContext(ctx, cache.query, vals...)
}
if err != nil {
return errors.Wrap(err, "record: unable to upsert entries")
}
if !cached {
entryUpsertCacheMut.Lock()
entryUpsertCache[key] = cache
entryUpsertCacheMut.Unlock()
}
return o.doAfterUpsertHooks(ctx, exec)
}
// Delete deletes a single Entry record with an executor.
// Delete will match against the primary key column to find the record to delete.
func (o *Entry) Delete(ctx context.Context, exec boil.ContextExecutor) (int64, error) {
if o == nil {
return 0, errors.New("record: no Entry provided for delete")
}
if err := o.doBeforeDeleteHooks(ctx, exec); err != nil {
return 0, err
}
args := queries.ValuesFromMapping(reflect.Indirect(reflect.ValueOf(o)), entryPrimaryKeyMapping)
sql := "DELETE FROM \"entries\" WHERE \"id\"=$1"
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, sql)
fmt.Fprintln(boil.DebugWriter, args...)
}
result, err := exec.ExecContext(ctx, sql, args...)
if err != nil {
return 0, errors.Wrap(err, "record: unable to delete from entries")
}
rowsAff, err := result.RowsAffected()
if err != nil {
return 0, errors.Wrap(err, "record: failed to get rows affected by delete for entries")
}
if err := o.doAfterDeleteHooks(ctx, exec); err != nil {
return 0, err
}
return rowsAff, nil
}
// DeleteAll deletes all matching rows.
func (q entryQuery) DeleteAll(ctx context.Context, exec boil.ContextExecutor) (int64, error) {
if q.Query == nil {
return 0, errors.New("record: no entryQuery provided for delete all")
}
queries.SetDelete(q.Query)
result, err := q.Query.ExecContext(ctx, exec)
if err != nil {
return 0, errors.Wrap(err, "record: unable to delete all from entries")
}
rowsAff, err := result.RowsAffected()
if err != nil {
return 0, errors.Wrap(err, "record: failed to get rows affected by deleteall for entries")
}
return rowsAff, nil
}
// DeleteAll deletes all rows in the slice, using an executor.
func (o EntrySlice) DeleteAll(ctx context.Context, exec boil.ContextExecutor) (int64, error) {
if o == nil {
return 0, errors.New("record: no Entry slice provided for delete all")
}
if len(o) == 0 {
return 0, nil
}
if len(entryBeforeDeleteHooks) != 0 {
for _, obj := range o {
if err := obj.doBeforeDeleteHooks(ctx, exec); err != nil {
return 0, err
}
}
}
var args []interface{}
for _, obj := range o {
pkeyArgs := queries.ValuesFromMapping(reflect.Indirect(reflect.ValueOf(obj)), entryPrimaryKeyMapping)
args = append(args, pkeyArgs...)
}
sql := "DELETE FROM \"entries\" WHERE " +
strmangle.WhereClauseRepeated(string(dialect.LQ), string(dialect.RQ), 1, entryPrimaryKeyColumns, len(o))
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, sql)
fmt.Fprintln(boil.DebugWriter, args)
}
result, err := exec.ExecContext(ctx, sql, args...)
if err != nil {
return 0, errors.Wrap(err, "record: unable to delete all from entry slice")
}
rowsAff, err := result.RowsAffected()
if err != nil {
return 0, errors.Wrap(err, "record: failed to get rows affected by deleteall for entries")
}
if len(entryAfterDeleteHooks) != 0 {
for _, obj := range o {
if err := obj.doAfterDeleteHooks(ctx, exec); err != nil {
return 0, err
}
}
}
return rowsAff, nil
}
// Reload refetches the object from the database
// using the primary keys with an executor.
func (o *Entry) Reload(ctx context.Context, exec boil.ContextExecutor) error {
ret, err := FindEntry(ctx, exec, o.ID)
if err != nil {
return err
}
*o = *ret
return nil
}
// ReloadAll refetches every row with matching primary key column values
// and overwrites the original object slice with the newly updated slice.
func (o *EntrySlice) ReloadAll(ctx context.Context, exec boil.ContextExecutor) error {
if o == nil || len(*o) == 0 {
return nil
}
slice := EntrySlice{}
var args []interface{}
for _, obj := range *o {
pkeyArgs := queries.ValuesFromMapping(reflect.Indirect(reflect.ValueOf(obj)), entryPrimaryKeyMapping)
args = append(args, pkeyArgs...)
}
sql := "SELECT \"entries\".* FROM \"entries\" WHERE " +
strmangle.WhereClauseRepeated(string(dialect.LQ), string(dialect.RQ), 1, entryPrimaryKeyColumns, len(*o))
q := queries.Raw(sql, args...)
err := q.Bind(ctx, exec, &slice)
if err != nil {
return errors.Wrap(err, "record: unable to reload all in EntrySlice")
}
*o = slice
return nil
}
// EntryExists checks if the Entry row exists.
func EntryExists(ctx context.Context, exec boil.ContextExecutor, iD int64) (bool, error) {
var exists bool
sql := "select exists(select 1 from \"entries\" where \"id\"=$1 limit 1)"
if boil.DebugMode {
fmt.Fprintln(boil.DebugWriter, sql)
fmt.Fprintln(boil.DebugWriter, iD)
}
row := exec.QueryRowContext(ctx, sql, iD)
err := row.Scan(&exists)
if err != nil {
return false, errors.Wrap(err, "record: unable to check if entries exists")
}
return exists, nil
}
|
sdmg15/GoodDAPP | src/lib/share/__tests__/generateReceiveShareObject.js | <reponame>sdmg15/GoodDAPP
import { generateReceiveShareObject, generateShareLink } from '../'
const isReceiveLink = generateShareLink('receive', { amount: '123' })
describe('generateReceiveShareObject', () => {
it(`should return an object for receipt with code, amount, to and from`, () => {
// Given
const title = 'Sending G$ via GoodDollar App'
const message = "<NAME>, You've got a request from <NAME> for 1 G$. To approve transfer open: "
// When
const shareObject = generateReceiveShareObject({ amount: '123' }, 100, '<NAME>', '<NAME>')
// Then
expect(shareObject.title).toBe(title)
expect(shareObject.message).toBe(message)
expect(shareObject.url).toMatch(isReceiveLink)
})
it(`should return an object for receipt with code, to and from`, () => {
// Given
const title = 'Sending G$ via GoodDollar App'
const message = "<NAME>, You've got a request from <NAME>. To approve transfer open: "
// When
const shareObject = generateReceiveShareObject({ amount: '123' }, 0, '<NAME>', '<NAME>')
// Then
expect(shareObject.title).toBe(title)
expect(shareObject.message).toBe(message)
expect(shareObject.url).toMatch(isReceiveLink)
})
it(`should return an object for receipt with code, amount and from`, () => {
// Given
const title = 'Sending G$ via GoodDollar App'
const message = "You've got a request from <NAME> for 1 G$. To approve transfer open: "
// When
const shareObject = generateReceiveShareObject({ amount: '123' }, '100', '', '<NAME>')
// Then
expect(shareObject.title).toBe(title)
expect(shareObject.message).toBe(message)
expect(shareObject.url).toMatch(isReceiveLink)
})
it(`should return an object for receipt with code and from`, () => {
// Given
const title = 'Sending G$ via GoodDollar App'
const message = "You've got a request from <NAME>. To approve transfer open: "
// When
const shareObject = generateReceiveShareObject({ amount: '123' }, 0, '', '<NAME>')
// Then
expect(shareObject.title).toBe(title)
expect(shareObject.message).toBe(message)
expect(shareObject.url).toMatch(isReceiveLink)
})
})
|
fieldenms/ | platform-pojo-bl/src/main/java/ua/com/fielden/platform/entity/annotation/CompanionObject.java | package ua.com.fielden.platform.entity.annotation;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import ua.com.fielden.platform.dao.IEntityDao;
import ua.com.fielden.platform.entity.AbstractEntity;
/**
* Annotation for specify a default controller for an domain entity.
*
* @author <NAME>
*
*/
@Retention(RetentionPolicy.RUNTIME)
@Target({ ElementType.TYPE })
public @interface CompanionObject {
Class<? extends IEntityDao<? extends AbstractEntity<?>>> value();
}
|
Andreynnt/2018_1_Drive | public/js/services/user-service.js | import {httpModule} from '../modules/http';
export class UserService {
checkAuth() {
this.loadMe((err, me) => {
if (err) {
console.dir(me);
console.log('Вы не авторизованы');
return;
}
console.log('me is', me);
alert('Добро пожаловать!');
});
}
loadMe(callback) {
httpModule.doGet({
url: '/user',
callback
});
}
loadUsers(firstManPos, amountOfPeople) {
return httpModule.promiseGet(`/leaders/${firstManPos}/${amountOfPeople}`);
}
logout() {
httpModule.doGet({
url: '/logout'
});
}
RegOrSignin(type, formData) {
if (type === 'register') {
httpModule.promisePost('/register', formData)
.then(response => alert('Ваш login: ' + response.user.login + ' и почта: ' + response.user.mail))
.catch(err => console.log(err));
} else if (type === 'login') {
return httpModule.promisePost('/signin', formData)
.then(response => {
alert('Привет ' + response.user.login + '!');
return response;
})
.catch(() => alert('Пользователь не существует'));
}
}
}
|
faisalsanto007/Codes | data final practice/selection sort.cpp | #include <stdio.h>
int min(int a[],int k,int n)
{
int i=k,l,m;
for(i=i+1 ;i<n;i++)
{
if(a[k]>a[i])
{
k=i;
}
}
return k;
}
int main()
{
int i,j,k,l,a[1000],n;
printf("Enter number of element: ");
scanf("%d",&n);
printf("Enter element: ");
for(i=0;i<n;i++)
scanf("%d",&a[i]);
for(i=0;i<n-1;i++)
{
l=min(a,i,n);
k=a[i];
a[i]=a[l];
a[l]=k;
}
for(i=0;i<n;i++)
printf("%d ",a[i]);
printf("\n");
}
|
andytubeee/jamhacks.ca | 2021/src/data/Navbar/Privacy.js | <filename>2021/src/data/Navbar/Privacy.js<gh_stars>0
const PrivacyNavData = [
{
label: 'Definitions',
id: 'definitions-section',
enabled: true,
},
{
label: 'Data',
id: 'data-section',
enabled: true,
},
{
label: 'Privacy',
id: 'privacy-section',
enabled: true,
},
{
label: 'Other',
id: 'other-section',
enabled: true,
},
{
label: 'Contact',
id: 'contact-section',
enabled: true,
},
];
export default PrivacyNavData;
|
ceekay1991/AliPayForDebug | AliPayForDebug/AliPayForDebug/AlipayWallet_Headers/GO2OStackedGridHeaderProtocol-Protocol.h | <filename>AliPayForDebug/AliPayForDebug/AlipayWallet_Headers/GO2OStackedGridHeaderProtocol-Protocol.h<gh_stars>1-10
//
// Generated by class-dump 3.5 (64 bit) (Debug version compiled Sep 17 2017 16:24:48).
//
// class-dump is Copyright (C) 1997-1998, 2000-2001, 2004-2015 by <NAME>.
//
#import "NSObject-Protocol.h"
@class GO2OCommonTabbar, GO2OStackedGridHeaderView;
@protocol GO2OStackedGridHeaderProtocol <NSObject>
@optional
- (void)stackedGridHeader:(GO2OStackedGridHeaderView *)arg1 tabbar:(GO2OCommonTabbar *)arg2 didSelectItemAtIndex:(long long)arg3 originIndex:(long long)arg4;
@end
|
wrldwzrd89/older-java-games | MasterMaze/src/com/puttysoftware/mastermaze/battle/BattleTarget.java | <filename>MasterMaze/src/com/puttysoftware/mastermaze/battle/BattleTarget.java
/* MasterMaze: An RPG
Copyright (C) 2011-2012 <NAME>
Any questions should be directed to the author via email at: <EMAIL>
*/
package com.puttysoftware.mastermaze.battle;
public enum BattleTarget {
SELF, ONE_ALLY, ONE_ENEMY, ALL_ALLIES, ALL_ENEMIES;
}
|
jayvdb/django-formidable | docs/tests/test_forms_field_validations.py | from copy import deepcopy
from . import validator, _load_fixture
def test_field_validations():
form = _load_fixture('0017_fields_validations.json')
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 0
# An empty list should still validate
form['fields'][0]['validations'] = []
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 0
# wrong type should trigger a type error
form['fields'][0]['validations'] = "something"
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 1
error = errors[0]
assert error.validator == 'type'
assert error.message == "'something' is not of type 'array'"
def _load_17_fields_validations():
form = _load_fixture('0017_fields_validations.json')
items = deepcopy(form['fields'][0]['validations'])
item = deepcopy(items[0])
return form, items, item
def test_field_validations_no_message():
form, items, no_message = _load_17_fields_validations()
# Removing the overwritten message shouldn't invalidate the field
del no_message['message']
form['fields'][0]['validations'] = [no_message]
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 0
def test_field_validations_no_type():
form, items, no_type = _load_17_fields_validations()
del no_type['type']
form['fields'][0]['validations'] = [no_type]
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 1
error = errors[0]
assert error.validator == 'required'
assert error.message == "'type' is a required property"
def test_field_validations_no_value():
form, items, no_value = _load_17_fields_validations()
del no_value['value']
form['fields'][0]['validations'] = [no_value]
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 1
error = errors[0]
assert error.validator == 'required'
assert error.message == "'value' is a required property"
# TODO: field validation grids
# I don't know if it's possible to validate the grid.
#
# For the record, here's the grid:
# * text: MINLENGTH, MAXLENGTH, REGEXP
# * paragraph: MINLENGTH, MAXLENGTH, REGEXP
# * date: GT, GTE, LT, LTE, EQ, NEQ, IS_AGE_ABOVE (>=), IS_AGE_UNDER (<),
# IS_DATE_IN_THE_PAST, IS_DATE_IN_THE_FUTURE
# * number: GT, GTE, LT, LTE, EQ, NEQ
availablele_validation_types = [
'EQ',
'GT',
'GTE',
'IS_AGE_ABOVE',
'IS_AGE_UNDER',
'IS_DATE_IN_THE_FUTURE',
'IS_DATE_IN_THE_PAST',
'LT',
'LTE',
'MAXLENGTH',
'MINLENGTH',
'NEQ',
'REGEXP'
]
def test_field_validations_type_ok():
form, items, values = _load_17_fields_validations()
for validation_type in availablele_validation_types:
values.update({"type": validation_type})
form['fields'][0]['validations'] = [values]
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 0
def test_field_validations_wrong_type():
form, items, values = _load_17_fields_validations()
values.update({"type": 'UNKNOWN'})
form['fields'][0]['validations'] = [values]
errors = sorted(validator.iter_errors(form), key=lambda e: e.path)
assert len(errors) == 1
error = errors[0]
assert error.message == f"'UNKNOWN' is not one of {availablele_validation_types}" # noqa
|
yogjiao/midou | routers/Show/Show.js | <gh_stars>0
import React from 'react'
import PageSpin from 'PageSpin/PageSpin.js'
import ScrollingSpin from 'ScrollingSpin/ScrollingSpin.js'
import Confirm from 'Confirm/Confirm.js'
import Prompt from 'Prompt/Prompt.js'
import {
FETCH_STATUS_NO_MORE_PRODUCT,
FETCH_SUCCESS,
BASE_STATIC_DIR,
BASE_PAGE_DIR,
FETCH_NICE_SHOW,
DELETE_NICE_SHOW,
PAGE_TO_PAGE_SIGNAL,
FETCH_GOOD,
PUT_TO_CART,
CUSTMER_SERVICE_ID
} from 'macros.js'
import {
getMiDouToken,
getUserIdFromMidouToken
} from 'commonApp.js'
import {fetchable, fetchAuth, fetchOption} from 'fetch.js'
import errors from 'errors.js'
let update = require('react-addons-update')
import {getParentByClass} from 'util.js'
import ua from 'uaParser.js'
import ImageLayout from 'ImageLayout.js'
import Hammer from 'hammerjs'
import ShareToSocialMedia from 'ShareToSocialMedia/ShareToSocialMedia.js'
import Swiper from 'Swiper'
import NiceShowlayout from 'NiceShowlayout/NiceShowlayout.js'
import MoreMenu from 'MoreMenu.js'
import {
backToNativePage,
sendSignalToOtherPagesByOc,
calloutNewWebview,
getUserInfoFromApp,
receiveNotificationsFromApp
} from 'webviewInterface.js'
import VideoPlayer from 'VideoPlayer/VideoPlayer.js'
let reactMixin = require('react-mixin')
import * as detailMixins from 'mixins/underwearDetail.js'
import UnderweardetailBuyStack from 'UnderweardetailBuyStack/UnderweardetailBuyStack.js'
import UnderwearSelectPanel from 'UnderwearSelectPanel/UnderwearSelectPanel.js'
import './Show.less'
class Show extends React.Component {
constructor(props, context) {
super(props, context);
this.state = {
isHiddenPageSpin: false,
isHiddenConfirm: true,
isHiddenMoreMenu: true,
showData: {
user: {},
goods: [],
img: [],
video: {}
},
//goodsSelectedId: null,
goodsSelectedIndex: 0,
promptMsg: '',
// for recommend underpants, it's the same to underwareDetail
buyActionModel: 0,
isHiddenSelectPanel: true,
size: 0,
allBase: [],
braSize: 0, // bra
baseSize: 0, // bra
category: 1, // 1：文胸，2:底裤，3:情趣
boxes: [], // tags
count: 1,
goods: {inventoryInfo:{allBase:[], allSize: [], inventory:{}}},
};
}
fetchShowData = () => {
let url = `${FETCH_NICE_SHOW}/${this.props.params.showId}`
this.setState({isHiddenPageSpin: false})
fetchOption(url)
.then((data) => {
if (data.rea == FETCH_SUCCESS) {
if (data.show.is_valid == 0) {
data.show.img = [`${BASE_STATIC_DIR}/img/audit.png`]
}
this.setState({showData: data.show})// goodsSelectedId: data.show.goods[0].id
this.fetchDetailData(data.show.goods[this.state.goodsSelectedIndex].id)
} else {
throw new Error(errors[data.rea])
}
})
.catch((error) => {
})
.then(()=>{
this.setState({
isHiddenPageSpin: true,
//isHiddenScrollingSpin: true
})
})
};
deleteNiceShow = () => {
let url = `${DELETE_NICE_SHOW}/${this.props.params.showId}`
this.setState({isHiddenPageSpin: false})
fetchAuth(url)
.then((data) => {
if (data.rea == FETCH_SUCCESS) {
this.setState({promptMsg: '删除成功'})
setTimeout(() => {
backToNativePage()
}, 3000)
let signal = {
signal: PAGE_TO_PAGE_SIGNAL.UPDATE_SHOWS
}
sendSignalToOtherPagesByOc(signal)
} else {
throw new Error(errors[data.rea])
}
})
.catch((error) => {
this.setState({promptMsg: error.message})
})
.then(()=>{
this.setState({
isHiddenPageSpin: true
})
this.refs['prompt'].show()
})
};
thisHandler = (e) => {
let target
if (target = getParentByClass(e.target, 'icon-ellipsis')) {
this.setState({isHiddenMoreMenu: false})
} else if (target = getParentByClass(e.target, 'icon-share')) {
this.setState({isHiddenMoreMenu: true})
this.refs['share'].show()
} else if (target = getParentByClass(e.target, 'icon-delete')) {
this.setState({isHiddenMoreMenu: true, isHiddenConfirm: false})
} else if (target = getParentByClass(e.target, 'matching-card')) {
let index = target.getAttribute('data-index')
this.setState({goodsSelectedIndex: index})
this.fetchDetailData(this.state.showData.goods[this.state.goodsSelectedIndex].id)
}
};
postDataToCartHandler = () => {
let data = this.getPostToCartData()
let url = `${PUT_TO_CART}/${this.state.buyActionModel}`
fetchAuth(url, {method: 'post', body: JSON.stringify(data)})
.then((data) => {
if (data.rea == FETCH_SUCCESS) {
if (this.state.buyActionModel == 1) {
// this.props.history.push()
// this.props.history.goForward()
if (ua.isApp()) {
calloutNewWebview({url:`${window.location.origin}${BASE_PAGE_DIR}/order-created/${data.cid}/${this.state.buyActionModel}`})
} else {
window.location.href = `${window.location.origin}${BASE_PAGE_DIR}/order-created/${data.cid}/${this.state.buyActionModel}`
}
} else {
this.setState({promptMsg: '商品已添加到购物车'})
}
} else {
this.setState({promptMsg: errors[data.rea]})
}
})
.catch((e) => {
this.setState({promptMsg: errors[e.rea]})
})
.then(() => {
this.refs['prompt'].show();
})
};
buyHandler = (e) => {
let target,
nextState
if (target = getParentByClass(e.target, 'con-server')) {
getUserInfoFromApp()
.then((data) => {
calloutNewWebview({url:`${window.location.origin}${BASE_PAGE_DIR}/im/${CUSTMER_SERVICE_ID}?productId=${this.state.showData.goods[this.state.goodsSelectedIndex].id}`})
})
.catch((error) => {
this.setState({promptMsg: errors[error.rea]})
this.refs['prompt'].show()
})
} else if (target = getParentByClass(e.target, 'push-to-cart')) {
nextState = update(this.state, {
isHiddenSelectPanel: {$set: false},
buyActionModel: {$set: 0}
})
} else if (target = getParentByClass(e.target, 'buy-now')) {
nextState = update(this.state, {
isHiddenSelectPanel: {$set: false},
buyActionModel: {$set: 1}
})
}
nextState && this.setState(nextState)
};
moreMenuHandler = (e) => {
let target
if (target = getParentByClass(e.target, 'cancel-selection')) {
this.setState({isHiddenMoreMenu: true})
}
};
confirmHandler = (e) => {
let target
if (target = getParentByClass(e.target, 'btn-cancel')) {
this.setState({isHiddenConfirm: true})
} else if (target = getParentByClass(e.target, 'btn-confirm')) {
this.setState({isHiddenConfirm: true})
this.deleteNiceShow()
}
};
fetchDetailData = (productId) => {
this.state.isFetching = true
//this.setState({isHiddenPageSpin: false})
let url = `${FETCH_GOOD}/${productId}`
fetchable(url)
.then((data) => {
if (data.rea == FETCH_STATUS_NO_MORE_PRODUCT) {
this.state.isHaveGoods = false
}
data.goods.inventoryInfo =
this.rebuildInventory(data.goods.inventory, data.goods.category)
delete data.goods.inventory
let schema = {
category: {$set: data.goods.category},
goods: {$set: data.goods},
isFetching:{$set: false},
isHiddenPageSpin: {$set: true},
hasLoadedData: {$set: true}
}
if (data.goods.category == '1') {
let keys = Object.keys(data.goods.inventoryInfo.allBase)
schema.allBase = {$set: keys}
schema.baseSize = {$set: keys[0]}
schema.braSize = {$set: data.goods.inventoryInfo.allBase[keys[0]][0]}
//nextState.boxes = this.rebuildBoxes(nextState.braSize, nextState.baseSize, nextState.goods.inventoryInfo.inventory)
} else {
let keys = Object.keys(data.goods.inventoryInfo.inventory)
schema.allSize = {$set: keys}
schema.size = {$set: keys[0]}
}
let nextState = update(this.state, schema)
this.setState(nextState)
//return [nextState.goods.id]
})
.catch((error) => {
this.setState({
isFetching: false,
isHiddenPageSpin: true
})
})
.then((ids) => {
if (getMiDouToken()) {
this.freshCollectionBtnState(ids)
}
})
};
componentDidMount = () => {
this.fetchShowData()
// this.bindGesture()
// // document.addEventListener('scroll', this.handleScroll);
//
//
var mySwiper = new Swiper('.matching-group', {
slideClass: 'matching-card'
});
receiveNotificationsFromApp((data, callback) => {
if (data.type == '2') {// refresh nices
this.refs['share'].show()
}
})
};
componentWillUnmount = () => {
};
render() {
let goodsInfo = {}
try {
goodsInfo = this.state.showData.goods[this.state.goodsSelectedIndex] || {}
} catch (e) {}
return (
<div className="show-container" onClick={this.thisHandler}>
<i className="iconfont icon-jubao" />
<div className="adjust-container">
<NiceShowlayout goodsSelectedId={goodsInfo.id}>
{
this.state.showData.video ?
<VideoPlayer {...this.state.showData.video} /> :
<ImageLayout images={this.state.showData.img}/>
}
<div className="user-wrap">
<div className="avatar" style={{backgroundImage: `url(${this.state.showData.user.headimg})`}}></div>
<div className="user-name single-ellipsis">{this.state.showData.user.name}</div>
<i className="iconfont icon-ellipsis" />
</div>
<div className="user-comment" dangerouslySetInnerHTML={{__html: this.state.showData.comment}}/>
<div className="matching-group">
<div className="swiper-wrapper">
{
this.state.showData.goods.map((item, index) => {
return (
<div
className={this.state.goodsSelectedIndex == index? 'matching-card on' : 'matching-card'}
data-index={index}
data-id={item.id}
>
<div className="card-bg" key={index} style={{backgroundImage: `url(${item.main_img})`}}></div>
</div>
)
})
}
</div>
</div>
<div className="underwear-wrap">
<div className="underwear-bg"
style={{backgroundImage: `url(${goodsInfo.main_img})`}}
></div>
<div className="underwear-name">{goodsInfo.name}</div>
<p className="underwear-price">¥ {goodsInfo.price}</p>
</div>
</NiceShowlayout>
<UnderweardetailBuyStack
buyHandler={this.buyHandler}
isCollected={this.state.goods.isCollected}
id={this.state.goods.id}
isHiddenCollection={true}
/>
</div>
<PageSpin isHidden={this.state.isHiddenPageSpin}/>
<Confirm isHidden={this.state.isHiddenConfirm} thisHandler={this.confirmHandler}/>
{
this.state.isHiddenMoreMenu ? '' : <MoreMenu thisHandler={this.moreMenuHandler} userId={this.state.showData.user.id}/>
}
<ShareToSocialMedia
ref="share"
url={window.location.href}
title={(this.state.showData.goods[0] || {}).name}
description={this.state.showData.comment}
imgUrl={this.state.showData.share_img}
/>
<Prompt msg={this.state.promptMsg} ref='prompt'/>
<UnderwearSelectPanel
isHidden={this.state.isHiddenSelectPanel}
allBase={this.state.allBase}
{...this.state}
selectHandler={this.selectHandler.bind(this)}
/>
</div>
)
}
}
// Home.childContextTypes = {
// pageSpin: React.PropTypes.node.isRequired
// }
// Home.contextTypes = {
// name: React.PropTypes.string.isRequired,
// //router: React.PropTypes.func.isRequired
// }
// Home.context = {
// //pageSpin: pageSpin
// }
reactMixin(Show.prototype, detailMixins)
module.exports = Show
|
farukranabappy89/google-ads-java | google-ads-stubs-v9/src/main/java/com/google/ads/googleads/v9/enums/RecommendationTypeProto.java | <filename>google-ads-stubs-v9/src/main/java/com/google/ads/googleads/v9/enums/RecommendationTypeProto.java
// Generated by the protocol buffer compiler. DO NOT EDIT!
// source: google/ads/googleads/v9/enums/recommendation_type.proto
package com.google.ads.googleads.v9.enums;
public final class RecommendationTypeProto {
private RecommendationTypeProto() {}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistryLite registry) {
}
public static void registerAllExtensions(
com.google.protobuf.ExtensionRegistry registry) {
registerAllExtensions(
(com.google.protobuf.ExtensionRegistryLite) registry);
}
static final com.google.protobuf.Descriptors.Descriptor
internal_static_google_ads_googleads_v9_enums_RecommendationTypeEnum_descriptor;
static final
com.google.protobuf.GeneratedMessageV3.FieldAccessorTable
internal_static_google_ads_googleads_v9_enums_RecommendationTypeEnum_fieldAccessorTable;
public static com.google.protobuf.Descriptors.FileDescriptor
getDescriptor() {
return descriptor;
}
private static com.google.protobuf.Descriptors.FileDescriptor
descriptor;
static {
java.lang.String[] descriptorData = {
"\n7google/ads/googleads/v9/enums/recommen" +
"dation_type.proto\022\035google.ads.googleads." +
"v9.enums\032\034google/api/annotations.proto\"\207" +
"\004\n\026RecommendationTypeEnum\"\354\003\n\022Recommenda" +
"tionType\022\017\n\013UNSPECIFIED\020\000\022\013\n\007UNKNOWN\020\001\022\023" +
"\n\017CAMPAIGN_BUDGET\020\002\022\013\n\007KEYWORD\020\003\022\013\n\007TEXT" +
"_AD\020\004\022\025\n\021TARGET_CPA_OPT_IN\020\005\022\037\n\033MAXIMIZE" +
"_CONVERSIONS_OPT_IN\020\006\022\027\n\023ENHANCED_CPC_OP" +
"T_IN\020\007\022\032\n\026SEARCH_PARTNERS_OPT_IN\020\010\022\032\n\026MA" +
"XIMIZE_CLICKS_OPT_IN\020\t\022\030\n\024OPTIMIZE_AD_RO" +
"TATION\020\n\022\025\n\021CALLOUT_EXTENSION\020\013\022\026\n\022SITEL" +
"INK_EXTENSION\020\014\022\022\n\016CALL_EXTENSION\020\r\022\026\n\022K" +
"EYWORD_MATCH_TYPE\020\016\022\026\n\022MOVE_UNUSED_BUDGE" +
"T\020\017\022\037\n\033FORECASTING_CAMPAIGN_BUDGET\020\020\022\026\n\022" +
"TARGET_ROAS_OPT_IN\020\021\022\030\n\024RESPONSIVE_SEARC" +
"H_AD\020\022\022 \n\034MARGINAL_ROI_CAMPAIGN_BUDGET\020\023" +
"B\354\001\n!com.google.ads.googleads.v9.enumsB\027" +
"RecommendationTypeProtoP\001ZBgoogle.golang" +
".org/genproto/googleapis/ads/googleads/v" +
"9/enums;enums\242\002\003GAA\252\002\035Google.Ads.GoogleA" +
"ds.V9.Enums\312\002\035Google\\Ads\\GoogleAds\\V9\\En" +
"ums\352\002!Google::Ads::GoogleAds::V9::Enumsb" +
"\006proto3"
};
descriptor = com.google.protobuf.Descriptors.FileDescriptor
.internalBuildGeneratedFileFrom(descriptorData,
new com.google.protobuf.Descriptors.FileDescriptor[] {
com.google.api.AnnotationsProto.getDescriptor(),
});
internal_static_google_ads_googleads_v9_enums_RecommendationTypeEnum_descriptor =
getDescriptor().getMessageTypes().get(0);
internal_static_google_ads_googleads_v9_enums_RecommendationTypeEnum_fieldAccessorTable = new
com.google.protobuf.GeneratedMessageV3.FieldAccessorTable(
internal_static_google_ads_googleads_v9_enums_RecommendationTypeEnum_descriptor,
new java.lang.String[] { });
com.google.api.AnnotationsProto.getDescriptor();
}
// @@protoc_insertion_point(outer_class_scope)
}
|
satoshun/truth-android | truth-android/src/main/java/com/github/satoshun/truth/android/api/animation/AnimatorSetSubject.java | <filename>truth-android/src/main/java/com/github/satoshun/truth/android/api/animation/AnimatorSetSubject.java
package com.github.satoshun.truth.android.api.animation;
import android.animation.AnimatorSet;
import android.annotation.TargetApi;
import com.google.common.truth.FailureStrategy;
import com.google.common.truth.SubjectFactory;
import static android.os.Build.VERSION_CODES.HONEYCOMB;
@TargetApi(HONEYCOMB)
public class AnimatorSetSubject extends AnimatorSubject<AnimatorSetSubject, AnimatorSet> {
public static final AnimatorSetSubjectFactory FACTORY = new AnimatorSetSubjectFactory();
public AnimatorSetSubject(FailureStrategy failureStrategy, AnimatorSet actual) {
super(failureStrategy, actual);
}
public AnimatorSetSubject isAnimatorCount(int count) {
isNotNull();
check().withFailureMessage("is animator count")
.that(actual().getChildAnimations())
.hasSize(count);
return myself();
}
private static class AnimatorSetSubjectFactory extends SubjectFactory<AnimatorSetSubject, AnimatorSet> {
@Override
public AnimatorSetSubject getSubject(FailureStrategy fs, AnimatorSet that) {
return new AnimatorSetSubject(fs, that);
}
}
}
|
shashwatsingh/addons-server | src/olympia/translations/__init__.py | from django.conf import settings
from django.utils.translation import trans_real
from jinja2.filters import do_dictsort
LOCALES = [(trans_real.to_locale(k).replace('_', '-'), v) for k, v in
do_dictsort(settings.LANGUAGES)]
|
BennyJane/java-demo | java-base-demo/src/main/java/org/example/com/java8Demo/DateDemo.java | <filename>java-base-demo/src/main/java/org/example/com/java8Demo/DateDemo.java
package org.example.com.java8Demo;
import java.time.*;
public class DateDemo {
public static void main(String[] args) {
methodTest();
}
static void methodTest() {
// Clock
// 替代了 System.currentTimeMillis() TimeZone.getDefault()
final Clock clock = Clock.systemUTC();
System.out.println(clock.instant()); // 当前时区的时间
System.out.println(clock.millis()); // 纳米时间
// LocalDate 获取时间的日期部分
final LocalDate date = LocalDate.now();
final LocalDate dateFromClock = LocalDate.now(clock);
System.out.println(date);
System.out.println(dateFromClock);
final LocalTime time = LocalTime.now();
final LocalTime timeFromCock = LocalTime.now( clock);
System.out.println(time);
System.out.println(timeFromCock);
// LocalDateTime 同时包含了LocalDate LocalTime的信息，但不包含ISO-8601日历系统中的时区信息
final LocalDateTime datetime = LocalDateTime.now();
final LocalDateTime datetimeFromClock = LocalDateTime.now(clock);
System.out.println(datetime);
System.out.println(datetimeFromClock);
// ZoneDateTime: 保存有ISO-8601日期系统的日期和时间，而且有时区信息
// Get the zoned date/time
final ZonedDateTime zonedDatetime = ZonedDateTime.now();
final ZonedDateTime zonedDatetimeFromClock = ZonedDateTime.now( clock );
final ZonedDateTime zonedDatetimeFromZone = ZonedDateTime.now( ZoneId.of( "America/Los_Angeles" ) );
System.out.println( zonedDatetime );
System.out.println( zonedDatetimeFromClock );
System.out.println( zonedDatetimeFromZone );
// Duration类，它持有的时间精确到秒和纳秒,可以很容易得计算两个日期之间的不同
// Get duration between two dates
final LocalDateTime from = LocalDateTime.of( 2014, Month.APRIL, 16, 0, 0, 0 );
final LocalDateTime to = LocalDateTime.of( 2015, Month.APRIL, 16, 23, 59, 59 );
final Duration duration = Duration.between( from, to );
System.out.println( "Duration in days: " + duration.toDays() );
System.out.println( "Duration in hours: " + duration.toHours() );
}
}
|
silvioedu/HackerRank-Python-Practice | basicDataTypes/FindTheRunnerUpScore.py | <reponame>silvioedu/HackerRank-Python-Practice
if __name__ == '__main__':
n = int(input())
arr = map(int, input().split())
lis = list(arr)
z = max(lis)
while max(lis) == z:
lis.remove(max(lis))
print(max(lis)) |
gubaojian/weexuikit | RenderCore/render/platform/SharedBuffer.cpp | /*
* Copyright (C) 2006, 2008 Apple Inc. All rights reserved.
* Copyright (C) Research In Motion Limited 2009-2010. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY APPLE COMPUTER, INC. ``AS IS'' AND ANY
* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
* PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL APPLE COMPUTER, INC. OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
* OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "render/platform/SharedBuffer.h"
// #include "flutter/common/threads.h"
#include "render/public/platform/Platform.h"
#include "render/wtf/unicode/UTF8.h"
#include "render/wtf/unicode/Unicode.h"
#include "third_party/skia/include/private/SkMalloc.h"
#undef SHARED_BUFFER_STATS
#ifdef SHARED_BUFFER_STATS
#include "render/wtf/DataLog.h"
#endif
namespace blink {
static const unsigned segmentSize = 0x1000;
static const unsigned segmentPositionMask = 0x0FFF;
static inline unsigned segmentIndex(unsigned position) {
return position / segmentSize;
}
static inline unsigned offsetInSegment(unsigned position) {
return position & segmentPositionMask;
}
static inline char* allocateSegment() {
return static_cast<char*>(fastMalloc(segmentSize));
}
static inline void freeSegment(char* p) {
fastFree(p);
}
#ifdef SHARED_BUFFER_STATS
static Mutex& statsMutex() {
DEFINE_STATIC_LOCAL(Mutex, mutex, ());
return mutex;
}
static HashSet<SharedBuffer*>& liveBuffers() {
DEFINE_STATIC_LOCAL(HashSet<SharedBuffer*>, buffers, ());
return buffers;
}
static bool sizeComparator(SharedBuffer* a, SharedBuffer* b) {
return a->size() > b->size();
}
static CString snippetForBuffer(SharedBuffer* sharedBuffer) {
const unsigned kMaxSnippetLength = 64;
char* snippet = 0;
unsigned snippetLength = std::min(sharedBuffer->size(), kMaxSnippetLength);
CString result = CString::newUninitialized(snippetLength, snippet);
const char* segment;
unsigned offset = 0;
while (unsigned segmentLength = sharedBuffer->getSomeData(segment, offset)) {
unsigned length = std::min(segmentLength, snippetLength - offset);
memcpy(snippet + offset, segment, length);
offset += segmentLength;
if (offset >= snippetLength)
break;
}
for (unsigned i = 0; i < snippetLength; ++i) {
if (!isASCIIPrintable(snippet[i]))
snippet[i] = '?';
}
return result;
}
static void printStats() {
MutexLocker locker(statsMutex());
Vector<SharedBuffer*> buffers;
for (HashSet<SharedBuffer*>::const_iterator iter = liveBuffers().begin();
iter != liveBuffers().end(); ++iter)
buffers.append(*iter);
std::sort(buffers.begin(), buffers.end(), sizeComparator);
dataLogF("---- Shared Buffer Stats ----\n");
for (size_t i = 0; i < buffers.size() && i < 64; ++i) {
CString snippet = snippetForBuffer(buffers[i]);
dataLogF("Buffer size=%8u %s\n", buffers[i]->size(), snippet.data());
}
}
static void didCreateSharedBuffer(SharedBuffer* buffer) {
MutexLocker locker(statsMutex());
liveBuffers().add(buffer);
Threads::UI()->PostTask(printStats);
}
static void willDestroySharedBuffer(SharedBuffer* buffer) {
MutexLocker locker(statsMutex());
liveBuffers().remove(buffer);
}
#endif
SharedBuffer::SharedBuffer()
: m_size(0), m_buffer(PurgeableVector::NotPurgeable) {
#ifdef SHARED_BUFFER_STATS
didCreateSharedBuffer(this);
#endif
}
SharedBuffer::SharedBuffer(size_t size)
: m_size(size), m_buffer(PurgeableVector::NotPurgeable) {
m_buffer.reserveCapacity(size);
m_buffer.grow(size);
#ifdef SHARED_BUFFER_STATS
didCreateSharedBuffer(this);
#endif
}
SharedBuffer::SharedBuffer(const char* data, int size)
: m_size(0), m_buffer(PurgeableVector::NotPurgeable) {
// FIXME: Use unsigned consistently, and check for invalid casts when calling
// into SharedBuffer from other code.
if (size < 0)
CRASH();
append(data, size);
#ifdef SHARED_BUFFER_STATS
didCreateSharedBuffer(this);
#endif
}
SharedBuffer::SharedBuffer(const char* data,
int size,
PurgeableVector::PurgeableOption purgeable)
: m_size(0), m_buffer(purgeable) {
// FIXME: Use unsigned consistently, and check for invalid casts when calling
// into SharedBuffer from other code.
if (size < 0)
CRASH();
append(data, size);
#ifdef SHARED_BUFFER_STATS
didCreateSharedBuffer(this);
#endif
}
SharedBuffer::SharedBuffer(const unsigned char* data, int size)
: m_size(0), m_buffer(PurgeableVector::NotPurgeable) {
// FIXME: Use unsigned consistently, and check for invalid casts when calling
// into SharedBuffer from other code.
if (size < 0)
CRASH();
append(reinterpret_cast<const char*>(data), size);
#ifdef SHARED_BUFFER_STATS
didCreateSharedBuffer(this);
#endif
}
SharedBuffer::~SharedBuffer() {
clear();
#ifdef SHARED_BUFFER_STATS
willDestroySharedBuffer(this);
#endif
}
PassRefPtr<SharedBuffer> SharedBuffer::adoptVector(Vector<char>& vector) {
RefPtr<SharedBuffer> buffer = create();
buffer->m_buffer.adopt(vector);
buffer->m_size = buffer->m_buffer.size();
return buffer.release();
}
unsigned SharedBuffer::size() const {
return m_size;
}
const char* SharedBuffer::data() const {
mergeSegmentsIntoBuffer();
return m_buffer.data();
}
void SharedBuffer::append(PassRefPtr<SharedBuffer> data) {
const char* segment;
size_t position = 0;
while (size_t length = data->getSomeData(segment, position)) {
append(segment, length);
position += length;
}
}
void SharedBuffer::append(const char* data, unsigned length) {
ASSERT(isLocked());
if (!length)
return;
ASSERT(m_size >= m_buffer.size());
unsigned positionInSegment = offsetInSegment(m_size - m_buffer.size());
m_size += length;
if (m_size <= segmentSize) {
// No need to use segments for small resource data.
m_buffer.append(data, length);
return;
}
char* segment;
if (!positionInSegment) {
segment = allocateSegment();
m_segments.append(segment);
} else
segment = m_segments.last() + positionInSegment;
unsigned segmentFreeSpace = segmentSize - positionInSegment;
unsigned bytesToCopy = std::min(length, segmentFreeSpace);
for (;;) {
memcpy(segment, data, bytesToCopy);
if (static_cast<unsigned>(length) == bytesToCopy)
break;
length -= bytesToCopy;
data += bytesToCopy;
segment = allocateSegment();
m_segments.append(segment);
bytesToCopy = std::min(length, segmentSize);
}
}
void SharedBuffer::append(const Vector<char>& data) {
append(data.data(), data.size());
}
void SharedBuffer::clear() {
for (unsigned i = 0; i < m_segments.size(); ++i)
freeSegment(m_segments[i]);
m_segments.clear();
m_size = 0;
m_buffer.clear();
}
PassRefPtr<SharedBuffer> SharedBuffer::copy() const {
RefPtr<SharedBuffer> clone(adoptRef(new SharedBuffer));
clone->m_size = m_size;
clone->m_buffer.reserveCapacity(m_size);
clone->m_buffer.append(m_buffer.data(), m_buffer.size());
if (!m_segments.isEmpty()) {
const char* segment = 0;
unsigned position = m_buffer.size();
while (unsigned segmentSize = getSomeData(segment, position)) {
clone->m_buffer.append(segment, segmentSize);
position += segmentSize;
}
ASSERT(position == clone->size());
}
return clone.release();
}
void SharedBuffer::mergeSegmentsIntoBuffer() const {
unsigned bufferSize = m_buffer.size();
if (m_size > bufferSize) {
m_buffer.reserveCapacity(m_size);
unsigned bytesLeft = m_size - bufferSize;
for (unsigned i = 0; i < m_segments.size(); ++i) {
unsigned bytesToCopy = std::min(bytesLeft, segmentSize);
m_buffer.append(m_segments[i], bytesToCopy);
bytesLeft -= bytesToCopy;
freeSegment(m_segments[i]);
}
m_segments.clear();
}
}
unsigned SharedBuffer::getSomeData(const char*& someData,
unsigned position) const {
ASSERT(isLocked());
unsigned totalSize = size();
if (position >= totalSize) {
someData = 0;
return 0;
}
ASSERT_WITH_SECURITY_IMPLICATION(position < m_size);
unsigned consecutiveSize = m_buffer.size();
if (position < consecutiveSize) {
someData = m_buffer.data() + position;
return consecutiveSize - position;
}
position -= consecutiveSize;
unsigned segments = m_segments.size();
unsigned maxSegmentedSize = segments * segmentSize;
unsigned segment = segmentIndex(position);
if (segment < segments) {
unsigned bytesLeft = totalSize - consecutiveSize;
unsigned segmentedSize = std::min(maxSegmentedSize, bytesLeft);
unsigned positionInSegment = offsetInSegment(position);
someData = m_segments[segment] + positionInSegment;
return segment == segments - 1 ? segmentedSize - position
: segmentSize - positionInSegment;
}
ASSERT_NOT_REACHED();
return 0;
}
sk_sp<SkData> SharedBuffer::getAsSkData() const {
unsigned bufferLength = size();
char* buffer = static_cast<char*>(sk_malloc_throw(bufferLength));
const char* segment = 0;
unsigned position = 0;
while (unsigned segmentSize = getSomeData(segment, position)) {
memcpy(buffer + position, segment, segmentSize);
position += segmentSize;
}
if (position != bufferLength) {
ASSERT_NOT_REACHED();
// Don't return the incomplete SkData.
return nullptr;
}
return SkData::MakeFromMalloc(buffer, bufferLength);
}
bool SharedBuffer::lock() {
return m_buffer.lock();
}
void SharedBuffer::unlock() {
mergeSegmentsIntoBuffer();
m_buffer.unlock();
}
bool SharedBuffer::isLocked() const {
return m_buffer.isLocked();
}
} // namespace blink
|
PeterDinda/palacios | misc/network_servers/vtl/debug.cc | #include "debug.h"
#include <time.h>
#include <stdio.h>
#include <stdarg.h>
static FILE * logfile = NULL;
static int debug_on = 0;
int vtl_debug_init(string logfilename, int debug_enable) {
debug_on = debug_enable;
logfile = fopen(logfilename.c_str(), "w+");
return 0;
}
void vtl_debug(const char * fmt, ...) {
if (debug_on) {
va_list args;
time_t dbgt;
struct tm * time_data;
char time_str[200];
time(&dbgt);
time_data = localtime(&dbgt);
strftime(time_str, sizeof(time_str), "%a %b %d %r %Y : ", time_data);
fprintf(logfile, "%s", time_str);
va_start(args, fmt);
vfprintf(logfile, fmt, args);
va_end(args);
fflush(logfile);
}
}
|
popematt/ion-java | test/com/amazon/ion/impl/UnifiedInputStreamXTest.java | <reponame>popematt/ion-java
/*
* Copyright 2007-2019 Amazon.com, Inc. or its affiliates. All Rights Reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License").
* You may not use this file except in compliance with the License.
* A copy of the License is located at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* or in the "license" file accompanying this file. This file is distributed
* on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
* express or implied. See the License for the specific language governing
* permissions and limitations under the License.
*/
package com.amazon.ion.impl;
import org.junit.Assert;
import org.junit.Test;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
public class UnifiedInputStreamXTest extends Assert {
@Test
public void testReadExactlyAvailable() throws Exception {
class TestInputStream extends InputStream {
int remaining = 10;
@Override
public int read() throws IOException {
throw new UnsupportedOperationException();
}
@Override
public int read(byte[] b, int off, int len) throws IOException {
if (remaining == 0) {
throw new AssertionError("Unexpected call to read");
}
int amount = len;
if (amount > remaining) {
amount = remaining;
}
for (int i = off; i < (off + amount); i++) {
b[i] = (byte) 0xFF;
}
remaining -= amount;
return amount;
}
}
TestInputStream is = new TestInputStream();
UnifiedInputStreamX uix = UnifiedInputStreamX.makeStream(is);
byte[] expected = new byte[10];
Arrays.fill(expected, (byte) 0xFF);
byte[] actual = new byte[10];
int read = uix.read(actual, 0, actual.length);
assertArrayEquals(expected, actual);
}
}
|
tangya3158613488/Java | exercise20_1_4/Example6.java | package exercise20_1_4;
public class Example6 {
public static void main(String args[]){
int elements[]={1,2,3,4};
int hold[]={10,9,8,7,6,5,4,3,2,1};
System.arraycopy(elements, 0, hold, 0, elements.length);
System.out.println("长度为："+hold.length);
for(int i=0; i < hold.length; i++)
System.out.print(" "+hold[i]);
}
}
|
restapicoding/VMware-SDK | samples/vsphere/common/vapiconnect.py | """
* *******************************************************
* Copyright (c) VMware, Inc. 2016. All Rights Reserved.
* SPDX-License-Identifier: MIT
* *******************************************************
*
* DISCLAIMER. THIS PROGRAM IS PROVIDED TO YOU "AS IS" WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN,
* EXPRESS OR IMPLIED. THE AUTHOR SPECIFICALLY DISCLAIMS ANY IMPLIED
* WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY,
* NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE.
"""
__author__ = 'VMware, Inc.'
__copyright__ = 'Copyright 2016 VMware, Inc. All rights reserved.'
import requests
from com.vmware.cis_client import Session
from vmware.vapi.lib.connect import get_requests_connector
from vmware.vapi.security.session import create_session_security_context
from vmware.vapi.security.user_password import \
create_user_password_security_context
from vmware.vapi.stdlib.client.factories import StubConfigurationFactory
def get_jsonrpc_endpoint_url(host):
# The URL for the stub requests are made against the /api HTTP endpoint
# of the vCenter system.
return "https://{}/api".format(host)
def connect(host, user, pwd, skip_verification=False, cert_path=None, suppress_warning=True):
"""
Create an authenticated stub configuration object that can be used to issue
requests against vCenter.
Returns a stub_config that stores the session identifier that can be used
to issue authenticated requests against vCenter.
"""
host_url = get_jsonrpc_endpoint_url(host)
session = requests.Session()
if skip_verification:
session = create_unverified_session(session, suppress_warning)
elif cert_path:
session.verify = cert_path
connector = get_requests_connector(session=session, url=host_url)
stub_config = StubConfigurationFactory.new_std_configuration(connector)
return login(stub_config, user, pwd)
def login(stub_config, user, pwd):
"""
Create an authenticated session with vCenter.
Returns a stub_config that stores the session identifier that can be used
to issue authenticated requests against vCenter.
"""
# Pass user credentials (user/password) in the security context to
# authenticate.
user_password_security_context = create_user_password_security_context(user,
pwd)
stub_config.connector.set_security_context(user_password_security_context)
# Create the stub for the session service and login by creating a session.
session_svc = Session(stub_config)
session_id = session_svc.create()
# Successful authentication. Store the session identifier in the security
# context of the stub and use that for all subsequent remote requests
session_security_context = create_session_security_context(session_id)
stub_config.connector.set_security_context(session_security_context)
return stub_config
def logout(stub_config):
"""
Delete session with vCenter.
"""
if stub_config:
session_svc = Session(stub_config)
session_svc.delete()
def create_unverified_session(session, suppress_warning=True):
"""
Create a unverified session to disable the server certificate verification.
This is not recommended in production code.
"""
session.verify = False
if suppress_warning:
# Suppress unverified https request warnings
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
return session
|
pauxy-qmc/pauxy | pauxy/thermal_propagation/continuous.py | import cmath
import math
import numpy
import scipy.sparse.linalg
import sys
import time
from pauxy.estimators.thermal import one_rdm_from_G, inverse_greens_function_qr
from pauxy.propagation.operations import kinetic_real
from pauxy.thermal_propagation.planewave import PlaneWave
from pauxy.thermal_propagation.generic import GenericContinuous
from pauxy.thermal_propagation.hubbard import HubbardContinuous
from pauxy.utils.linalg import exponentiate_matrix
class Continuous(object):
"""Propagator for generic many-electron Hamiltonian.
Uses continuous HS transformation for exponential of two body operator.
Parameters
----------
options : dict
Propagator input options.
qmc : :class:`pauxy.qmc.options.QMCOpts`
QMC options.
system : :class:`pauxy.system.System`
System object.
trial : :class:`pauxy.trial_wavefunctioin.Trial`
Trial wavefunction object.
verbose : bool
If true print out more information during setup.
"""
def __init__(self, options, qmc, system, trial, verbose=False, lowrank=False):
if verbose:
print("# Parsing continuous propagator input options.")
print("# Using continuous Hubbar--Stratonovich transformations.")
# Input options
self.hs_type = 'continuous'
self.exp_nmax = options.get('expansion_order', 6)
optimised = options.get('optimised', True)
# Derived Attributes
self.dt = qmc.dt
self.sqrt_dt = qmc.dt**0.5
self.isqrt_dt = 1j*self.sqrt_dt
self.nfb_trig = 0
self.lowrank = lowrank
self.propagator = get_continuous_propagator(system, trial, qmc,
options=options,
verbose=verbose)
# Mean field shifted one-body propagator
self.mu = system.mu
self.propagator.construct_one_body_propagator(system, qmc.dt)
self.BH1 = self.propagator.BH1
self.BT = trial.dmat
self.BTinv = trial.dmat_inv
self.BT_BP = None
self.mf_const_fac = cmath.exp(-self.dt*self.propagator.mf_core)
self.nstblz = qmc.nstblz
self.ebound = (2.0/self.dt)**0.5
self.mean_local_energy = 0
self.free_projection = options.get('free_projection', False)
self.force_bias = options.get('force_bias', True)
if self.free_projection:
if verbose:
print("# Using free projection.")
print("# Setting force_bias to False with free projection.")
self.force_bias = options.get('force_bias', False)
self.propagate_walker = self.propagate_walker_free
else:
if verbose:
print("# Using phaseless approximation.")
if self.force_bias:
print("# Setting force bias to %r."%self.force_bias)
self.propagate_walker = self.propagate_walker_phaseless
if verbose:
print ("# Finished setting up propagator.")
def two_body_propagator(self, walker, system, trial):
r"""Continuous Hubbard-Statonovich transformation.
Parameters
----------
walker : :class:`pauxy.walker.Walker` walker object to be updated. On
output we have acted on phi by B_V(x).
system : :class:`pauxy.system.System`
System object.
trial : :class:`pauxy.trial_wavefunctioin.Trial`
Trial wavefunction object.
"""
# Normally distrubted auxiliary fields.
xi = numpy.random.normal(0.0, 1.0, system.nfields)
if self.force_bias:
P = one_rdm_from_G(walker.G)
xbar = self.propagator.construct_force_bias(system, P, trial)
else:
xbar = numpy.zeros(xi.shape, dtype=numpy.complex128)
for i in range(system.nfields):
if numpy.absolute(xbar[i]) > 1.0:
# if self.nfb_trig < 10:
# print("# Rescaling force bias is triggered")
# print("# Warning will only be printed 10 times on root.")
self.nfb_trig += 1
xbar[i] /= numpy.absolute(xbar[i])
# Constant factor arising from shifting the propability distribution.
cfb = xi.dot(xbar) - 0.5*xbar.dot(xbar)
xshifted = xi - xbar
# Constant factor arising from force bias and mean field shift
cmf = -self.sqrt_dt * xshifted.dot(self.propagator.mf_shift)
# Operator terms contributing to propagator.
VHS = self.propagator.construct_VHS(system, xshifted)
return (cmf, cfb, xshifted, VHS)
def estimate_eshift(self, walker):
return 0.0
def exponentiate(self, VHS, debug=False):
"""Apply exponential propagator of the HS transformation
Parameters
----------
system :
system class
phi : numpy array
a state
VHS : numpy array
HS transformation potential
Returns
-------
phi : numpy array
Exp(VHS) * phi
"""
# JOONHO: exact exponential
# copy = numpy.copy(phi)
# phi = scipy.linalg.expm(VHS).dot(copy)
phi = numpy.identity(VHS.shape[0], dtype = numpy.complex128)
if debug:
copy = numpy.copy(phi)
c2 = scipy.linalg.expm(VHS).dot(copy)
Temp = numpy.identity(VHS.shape[0], dtype = numpy.complex128)
for n in range(1, self.exp_nmax+1):
Temp = VHS.dot(Temp) / n
phi += Temp
if debug:
print("DIFF: {: 10.8e}".format((c2 - phi).sum() / c2.size))
return phi
def propagate_walker_free(self, system, walker, trial, eshift=0):
r"""Free projection for continuous HS transformation.
.. Warning::
Currently not implemented.
Parameters
----------
walker : :class:`walker.Walker`
Walker object to be updated. on output we have acted on
:math:`|\phi_i\rangle` by :math:`B` and updated the weight
appropriately. Updates inplace.
state : :class:`state.State`
Simulation state.
"""
(cmf, cfb, xmxbar, VHS) = self.two_body_propagator(walker, system, trial)
BV = self.exponentiate(VHS)
B = numpy.array([BV.dot(self.BH1[0]),BV.dot(self.BH1[1])])
B = numpy.array([self.BH1[0].dot(B[0]),self.BH1[1].dot(B[1])])
# Compute determinant ratio det(1+A')/det(1+A).
# 1. Current walker's green's function.
G = walker.greens_function(trial, inplace=False)
# 2. Compute updated green's function.
walker.stack.update_new(B)
walker.greens_function(trial, inplace=True)
# 3. Compute det(G/G')
M0 = [scipy.linalg.det(G[0], check_finite=False),
scipy.linalg.det(G[1], check_finite=False)]
Mnew = [scipy.linalg.det(walker.G[0], check_finite=False),
scipy.linalg.det(walker.G[1], check_finite=False)]
# Could save M0 rather than recompute.
try:
# Could save M0 rather than recompute.
oratio = (M0[0] * M0[1]) / (Mnew[0] * Mnew[1])
walker.ot = 1.0
# Constant terms are included in the walker's weight.
(magn, phase) = cmath.polar(cmath.exp(cmf+cfb)*oratio)
walker.weight *= magn
walker.phase *= cmath.exp(1j*phase)
except ZeroDivisionError:
walker.weight = 0.0
def propagate_walker_phaseless(self, system, walker, trial, eshift=0):
r"""Propagate walker using phaseless approximation.
Uses importance sampling and the hybrid method.
Parameters
----------
walker : :class:`walker.Walker`
Walker object to be updated. On output we have acted on phi with the
propagator B(x), and updated the weight appropriately. Updates
inplace.
system : :class:`pauxy.system.System`
System object.
trial : :class:`pauxy.trial_wavefunctioin.Trial`
Trial wavefunction object.
"""
(cmf, cfb, xmxbar, VHS) = self.two_body_propagator(walker,
system,
trial)
BV = self.exponentiate(VHS)
B = numpy.array([BV.dot(self.BH1[0]),BV.dot(self.BH1[1])])
B = numpy.array([self.BH1[0].dot(B[0]),self.BH1[1].dot(B[1])])
# Compute determinant ratio det(1+A')/det(1+A).
# 1. Current walker's green's function.
tix = walker.stack.ntime_slices
# 2. Compute updated green's function.
walker.stack.update_new(B)
walker.greens_function(None, slice_ix=tix, inplace=True)
# 3. Compute det(G/G')
M0 = walker.M0
Mnew = [scipy.linalg.det(walker.G[0], check_finite=False),
scipy.linalg.det(walker.G[1], check_finite=False)]
try:
# Could save M0 rather than recompute.
oratio = (M0[0] * M0[1]) / (Mnew[0] * Mnew[1])
# Might want to cap this at some point
hybrid_energy = cmath.log(oratio) + cfb + cmf
Q = cmath.exp(hybrid_energy)
expQ = self.mf_const_fac * Q
(magn, phase) = cmath.polar(expQ)
if not math.isinf(magn):
# Determine cosine phase from Arg(det(1+A'(x))/det(1+A(x))).
# Note this doesn't include exponential factor from shifting
# propability distribution.
dtheta = cmath.phase(cmath.exp(hybrid_energy-cfb))
cosine_fac = max(0, math.cos(dtheta))
walker.weight *= magn * cosine_fac
walker.M0 = Mnew
else:
walker.weight = 0.0
except ZeroDivisionError:
walker.weight = 0.0
def get_continuous_propagator(system, trial, qmc, options={}, verbose=False):
"""Wrapper to select propagator class.
Parameters
----------
options : dict
Propagator input options.
qmc : :class:`pauxy.qmc.QMCOpts` class
Trial wavefunction input options.
system : class
System class.
trial : class
Trial wavefunction object.
Returns
-------
propagator : class or None
Propagator object.
"""
if system.name == "UEG":
propagator = PlaneWave(system, trial, qmc,
options=options,
verbose=verbose)
elif system.name == "Hubbard":
propagator = HubbardContinuous(system, trial, qmc,
options=options,
verbose=verbose)
elif system.name == "Generic":
propagator = GenericContinuous(system, trial, qmc,
options=options,
verbose=verbose)
else:
propagator = None
return propagator
|
nowkoai/test | ee/spec/features/groups/analytics/ci_cd_analytics_spec.rb | # frozen_string_literal: true
require 'spec_helper'
RSpec.describe 'Group CI/CD Analytics', :js do
let_it_be(:user) { create(:user) }
let_it_be_with_refind(:group) { create(:group) }
let_it_be(:subgroup) { create(:group, parent: group ) }
let_it_be(:project_1) { create(:project, group: group) }
let_it_be(:project_2) { create(:project, group: group) }
let_it_be(:project_3) { create(:project, group: subgroup) }
let_it_be(:unrelated_project) { create(:project) }
let_it_be(:releases) { create_list(:release, 10, project: project_1) }
let_it_be(:releases) { create_list(:release, 5, project: project_3) }
let_it_be(:unrelated_release) { create(:release, project: unrelated_project) }
before do
stub_licensed_features(group_ci_cd_analytics: true, dora4_analytics: true)
group.add_reporter(user)
sign_in(user)
visit group_analytics_ci_cd_analytics_path(group)
wait_for_requests
end
it 'renders statistics about release within the group', :aggregate_failures do
within '[data-testid="release-stats-card"]' do
expect(page).to have_content 'Releases All time'
expect(page).to have_content '15 Releases 67% Projects with releases'
end
end
shared_examples 'a DORA chart' do |selector, title|
it "render the #{title} charts", :aggregate_failures do
click_link(title)
within selector do
expect(page).to have_content title
expect(page).to have_content 'Last week Last month Last 90 days'
expect(page).to have_content 'Date range:'
end
end
end
describe 'DORA charts' do
it_behaves_like 'a DORA chart', '[data-testid="deployment-frequency-charts"]', 'Deployment frequency'
it_behaves_like 'a DORA chart', '[data-testid="lead-time-charts"]', 'Lead time'
end
end
|
Dazzed/dental-front | app/containers/AdminManagePage/actions.js | <gh_stars>0
import {
CHANGE_PAGE_TITLE,
FETCH_ACCOUNT_MANAGERS,
SELECT_MANAGER,
TOGGLE_ADDING_MANAGER,
ADD_MANAGER,
TOGGLE_EDITING_MANAGER,
EDIT_MANAGER,
FETCH_SERVICES_REQUEST,
ADD_SERVICE_REQUEST,
DELETE_SERVICE_REQUEST,
TOGGLE_ADD_SERVICE,
} from './constants';
export function changePageTitle (payload) {
return {
type: CHANGE_PAGE_TITLE,
payload,
};
}
export function fetchAccountManagers() {
return {
type: FETCH_ACCOUNT_MANAGERS
};
}
export function selectManager(manager) {
return {
type: SELECT_MANAGER,
payload: manager,
};
}
export function toggleAddingManager(value) {
return {
type: TOGGLE_ADDING_MANAGER,
payload: value,
}
}
export function addManager(values) {
return {
type: ADD_MANAGER,
payload: values,
}
}
export function toggleEditingManager(manager) {
return {
type: TOGGLE_EDITING_MANAGER,
payload: manager
};
}
export function editManager(values) {
return {
type: EDIT_MANAGER,
payload: values
};
}
export function fetchServices() {
return {
type: FETCH_SERVICES_REQUEST,
}
}
export function addService(service) {
return {
type: ADD_SERVICE_REQUEST,
payload: service,
};
}
export function deleteService(service) {
return {
type: DELETE_SERVICE_REQUEST,
payload: service,
};
}
export function toggleAddService(value) {
return {
type: TOGGLE_ADD_SERVICE,
payload: value,
}
}
|
photo/mobile-android | app/src/com/trovebox/android/app/ImageFragment.java | <filename>app/src/com/trovebox/android/app/ImageFragment.java
package com.trovebox.android.app;
import android.os.Bundle;
import android.support.v4.app.Fragment;
import android.view.Gravity;
import android.view.View;
import android.view.ViewGroup;
import android.widget.ImageView;
import android.widget.LinearLayout;
import android.widget.LinearLayout.LayoutParams;
import android.widget.TextView;
import com.trovebox.android.common.fragment.common.CommonFragment;
import com.trovebox.android.common.util.CommonUtils;
public final class ImageFragment extends CommonFragment {
int imageResourceId;
int contentResourceId;
private static final String KEY_CONTENT = "ImageFragment:imageResourceId";
int mNum;
public static Fragment newInstance(int i, int content) {
ImageFragment f = new ImageFragment();
f.imageResourceId = i;
f.contentResourceId = content;
return f;
}
@Override
public void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
if ((savedInstanceState != null) && savedInstanceState.containsKey(KEY_CONTENT)) {
imageResourceId = savedInstanceState.getInt(KEY_CONTENT);
}
}
@Override
public View onCreateView(org.holoeverywhere.LayoutInflater inflater, ViewGroup container,
Bundle savedInstanceState) {
TextView text = new TextView(getActivity());
text.setGravity(Gravity.CENTER);
text.setText(getString(contentResourceId));
text.setTextSize(10 * getResources().getDisplayMetrics().density);
int padding = (int) getResources().getDimensionPixelSize(R.dimen.activity_intro_margin);
text.setPadding(padding, padding, padding, padding);
ImageView image = new ImageView(getActivity());
image.setImageResource(imageResourceId);
LinearLayout layout = new LinearLayout(getActivity());
layout.setOrientation(LinearLayout.VERTICAL);
if (CommonUtils.isFroyoOrHigher()) {
layout.setLayoutParams(new LayoutParams(LayoutParams.MATCH_PARENT,
LayoutParams.MATCH_PARENT));
} else {
layout.setLayoutParams(new LayoutParams(LayoutParams.FILL_PARENT,
LayoutParams.FILL_PARENT));
}
layout.setGravity(Gravity.CENTER);
layout.addView(image);
layout.addView(text);
return layout;
}
@Override
public void onSaveInstanceState(Bundle outState) {
super.onSaveInstanceState(outState);
outState.putInt(KEY_CONTENT, imageResourceId);
}
}
|
GnaneshKunal/unix-programming | 14_7.c | <filename>14_7.c
#include <stdio.h>
#include <unistd.h>
#include <signal.h>
#include <fcntl.h>
#include <stdlib.h>
int lock_reg(int fd, int cmd, int type, off_t offset, int whence, off_t len);
#define FILE_MODE (S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)
#define writew_lock(fd, offset, whence, len) lock_reg(fd, F_SETLK, F_WRLCK, offset, whence, len)
static sigset_t oldmask, newmask, zeromask;
static volatile sig_atomic_t sigflag;
static void sig_fn(int signo) {
sigflag = 1;
}
int lock_reg(int fd, int cmd, int type, off_t offset, int whence, off_t len) {
struct flock lock;
lock.l_type = type; //F_RWLOCK, F_WRLOCK, F_UNLCK
lock.l_whence = whence; //byte offset, relative to l_whence
lock.l_start = offset; //SEEK_SET, SEEK_CUR, SEEK_END
lock.l_len = len; //bytes(0 means to EOF)
return (fcntl(fd, cmd, &lock));
}
void TELL_WAIT(void) {
if(signal(SIGUSR1, sig_fn) == SIG_ERR) {
puts("signal SIGUSR1 error");
exit(1);
}
if (signal(SIGUSR2, sig_fn) == SIG_ERR) {
puts("signal SIGUSR2 error");
exit(1);
}
sigemptyset(&zeromask);
sigemptyset(&newmask);
sigaddset(&newmask, SIGUSR1);
sigaddset(&newmask, SIGUSR2);
if (sigprocmask(SIG_BLOCK, &newmask, &oldmask) < 0) {
puts("SIG_BLOCK error");
exit(1);
}
}
void WAIT_PARENT(void) {
while (sigflag == 0)
sigsuspend(&zeromask);
sigflag = 0;
if (sigprocmask(SIG_SETMASK, &oldmask, 0) < 0) {
puts("sigprocmask error");
exit(1);
}
}
void WAIT_CHILD(void) {
while (sigflag == 0)
sigsuspend(&zeromask);
sigflag = 0;
if(sigprocmask(SIG_SETMASK, &oldmask, 0) < 0) {
puts("sigprocmask error");
exit(1);
}
}
void TELL_PARENT(pid_t pid) {
kill(pid, SIGUSR2);
}
void TELL_CHILD(pid_t pid) {
kill(pid, SIGUSR1);
}
static void lockabyte(const char *name, int fd, off_t offset) {
if (writew_lock(fd, offset, SEEK_SET, 1) < 0) {
puts("write_lock error");
exit(1);
}
printf("%s: got the lock, byte %lld\n", name, (long long)offset);
}
int main(void) {
int fd;
pid_t pid;
//create a file and write two bytes to it
if ((fd = creat("templock", FILE_MODE)) < 0) {
puts("creat error");
exit(1);
}
if (write(fd, "ab", 2) != 2) {
puts("write error");
exit(1);
}
TELL_WAIT();
if ((pid = fork()) < 0) {
puts("fork error");
exit(1);
} else if (pid == 0) {
lockabyte("child", fd, 0);
TELL_PARENT(getppid());
WAIT_PARENT();
lockabyte("child", fd, 1);
} else {
lockabyte("parent", fd, 1);
TELL_CHILD(pid);
WAIT_CHILD();
lockabyte("parent", fd, 0);
}
exit(0);
} |
karthikswarna/cpg | src/main/java/de/fraunhofer/aisec/cpg/graph/statements/BreakStatement.java | <gh_stars>1-10
/*
* Copyright (c) 2020, Fraunhofer AISEC. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* $$$$$$\ $$$$$$$\ $$$$$$\
* $$ __$$\ $$ __$$\ $$ __$$\
* $$ / \__|$$ | $$ |$$ / \__|
* $$ | $$$$$$$ |$$ |$$$$\
* $$ | $$ ____/ $$ |\_$$ |
* $$ | $$\ $$ | $$ | $$ |
* \$$$$$ |$$ | \$$$$$ |
* \______/ \__| \______/
*
*/
package de.fraunhofer.aisec.cpg.graph.statements;
import java.util.Objects;
/**
* Statement used to interrupt further execution of a loop body and exit the respective loop
* context. Can have a loop label, e.g. in Java, to specify which of the nested loops should be
* broken out of.
*/
public class BreakStatement extends Statement {
private String label = null;
/**
* Specifies the label of the loop in a nested structure that this statement will 'break'
*
* @return the label
*/
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (!(o instanceof BreakStatement)) {
return false;
}
BreakStatement that = (BreakStatement) o;
return super.equals(that) && Objects.equals(label, that.label);
}
@Override
public int hashCode() {
return super.hashCode();
}
}
|
hangar18rip/backtotechtesting | go/internal/services/loadbalancer/backend_address_pool_address_resource_test.go | package loadbalancer_test
import (
"context"
"fmt"
"testing"
"github.com/Azure/azure-sdk-for-go/services/network/mgmt/2021-05-01/network"
"github.com/hashicorp/terraform-provider-azurerm/internal/acceptance"
"github.com/hashicorp/terraform-provider-azurerm/internal/acceptance/check"
"github.com/hashicorp/terraform-provider-azurerm/internal/acceptance/types"
"github.com/hashicorp/terraform-provider-azurerm/internal/clients"
"github.com/hashicorp/terraform-provider-azurerm/internal/services/loadbalancer/parse"
"github.com/hashicorp/terraform-provider-azurerm/internal/tf/pluginsdk"
"github.com/hashicorp/terraform-provider-azurerm/utils"
)
var _ types.TestResourceVerifyingRemoved = BackendAddressPoolAddressResourceTests{}
type BackendAddressPoolAddressResourceTests struct{}
func TestAccBackendAddressPoolAddressBasic(t *testing.T) {
data := acceptance.BuildTestData(t, "azurerm_lb_backend_address_pool_address", "test")
r := BackendAddressPoolAddressResourceTests{}
data.ResourceTest(t, r, []acceptance.TestStep{
{
Config: r.basic(data),
Check: acceptance.ComposeTestCheckFunc(
check.That(data.ResourceName).ExistsInAzure(r),
),
},
data.ImportStep(),
})
}
func TestAccBackendAddressPoolAddressRequiresImport(t *testing.T) {
data := acceptance.BuildTestData(t, "azurerm_lb_backend_address_pool_address", "test")
r := BackendAddressPoolAddressResourceTests{}
data.ResourceTest(t, r, []acceptance.TestStep{
{
Config: r.basic(data),
Check: acceptance.ComposeTestCheckFunc(
check.That(data.ResourceName).ExistsInAzure(r),
),
},
data.RequiresImportErrorStep(r.requiresImport),
})
}
func TestAccBackendAddressPoolAddressDisappears(t *testing.T) {
data := acceptance.BuildTestData(t, "azurerm_lb_backend_address_pool_address", "test")
r := BackendAddressPoolAddressResourceTests{}
data.ResourceTest(t, r, []acceptance.TestStep{
data.DisappearsStep(acceptance.DisappearsStepData{
Config: r.basic,
TestResource: r,
}),
})
}
func TestAccBackendAddressPoolAddressUpdate(t *testing.T) {
data := acceptance.BuildTestData(t, "azurerm_lb_backend_address_pool_address", "test")
r := BackendAddressPoolAddressResourceTests{}
data.ResourceTest(t, r, []acceptance.TestStep{
{
Config: r.basic(data),
Check: acceptance.ComposeTestCheckFunc(
check.That(data.ResourceName).ExistsInAzure(r),
),
},
data.ImportStep(),
{
Config: r.update(data),
Check: acceptance.ComposeTestCheckFunc(
check.That(data.ResourceName).ExistsInAzure(r),
),
},
data.ImportStep(),
})
}
func (BackendAddressPoolAddressResourceTests) Exists(ctx context.Context, client *clients.Client, state *pluginsdk.InstanceState) (*bool, error) {
id, err := parse.BackendAddressPoolAddressID(state.ID)
if err != nil {
return nil, err
}
pool, err := client.LoadBalancers.LoadBalancerBackendAddressPoolsClient.Get(ctx, id.ResourceGroup, id.LoadBalancerName, id.BackendAddressPoolName)
if err != nil {
return nil, fmt.Errorf("retrieving %s: %+v", *id, err)
}
if pool.BackendAddressPoolPropertiesFormat == nil {
return nil, fmt.Errorf("retrieving %s: `properties` was nil", *id)
}
if pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses != nil {
for _, address := range *pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses {
if address.Name == nil {
continue
}
if *address.Name == id.AddressName {
return utils.Bool(true), nil
}
}
}
return utils.Bool(false), nil
}
func (BackendAddressPoolAddressResourceTests) Destroy(ctx context.Context, client *clients.Client, state *pluginsdk.InstanceState) (*bool, error) {
id, err := parse.BackendAddressPoolAddressID(state.ID)
if err != nil {
return nil, err
}
pool, err := client.LoadBalancers.LoadBalancerBackendAddressPoolsClient.Get(ctx, id.ResourceGroup, id.LoadBalancerName, id.BackendAddressPoolName)
if err != nil {
return nil, fmt.Errorf("retrieving %s: %+v", *id, err)
}
if pool.BackendAddressPoolPropertiesFormat == nil {
return nil, fmt.Errorf("retrieving %s: `properties` was nil", *id)
}
addresses := make([]network.LoadBalancerBackendAddress, 0)
if pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses != nil {
addresses = *pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses
}
newAddresses := make([]network.LoadBalancerBackendAddress, 0)
for _, address := range addresses {
if address.Name == nil {
continue
}
if *address.Name != id.AddressName {
newAddresses = append(newAddresses, address)
}
}
pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses = &newAddresses
future, err := client.LoadBalancers.LoadBalancerBackendAddressPoolsClient.CreateOrUpdate(ctx, id.ResourceGroup, id.LoadBalancerName, id.BackendAddressPoolName, pool)
if err != nil {
return nil, fmt.Errorf("updating %s: %+v", *id, err)
}
if err := future.WaitForCompletionRef(ctx, client.LoadBalancers.LoadBalancerBackendAddressPoolsClient.Client); err != nil {
return nil, fmt.Errorf("waiting for update of %s: %+v", *id, err)
}
return utils.Bool(true), nil
}
// nolint unused - for future use
func (BackendAddressPoolAddressResourceTests) backendAddressPoolHasAddresses(expected int) acceptance.ClientCheckFunc {
return func(ctx context.Context, clients *clients.Client, state *pluginsdk.InstanceState) error {
id, err := parse.LoadBalancerBackendAddressPoolID(state.ID)
if err != nil {
return err
}
client := clients.LoadBalancers.LoadBalancerBackendAddressPoolsClient
pool, err := client.Get(ctx, id.ResourceGroup, id.LoadBalancerName, id.BackendAddressPoolName)
if err != nil {
return err
}
if pool.BackendAddressPoolPropertiesFormat == nil {
return fmt.Errorf("`properties` is nil")
}
if pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses == nil {
return fmt.Errorf("`properties.loadBalancerBackendAddresses` is nil")
}
actual := len(*pool.BackendAddressPoolPropertiesFormat.LoadBalancerBackendAddresses)
if actual != expected {
return fmt.Errorf("expected %d but got %d addresses", expected, actual)
}
return nil
}
}
func (t BackendAddressPoolAddressResourceTests) basic(data acceptance.TestData) string {
template := t.template(data)
return fmt.Sprintf(`
provider "azurerm" {
features {}
}
%s
resource "azurerm_lb_backend_address_pool_address" "test" {
name = "address"
backend_address_pool_id = azurerm_lb_backend_address_pool.test.id
virtual_network_id = azurerm_virtual_network.test.id
ip_address = "172.16.31.10"
}
`, template)
}
func (t BackendAddressPoolAddressResourceTests) requiresImport(data acceptance.TestData) string {
template := t.basic(data)
return fmt.Sprintf(`
%s
resource "azurerm_lb_backend_address_pool_address" "import" {
name = azurerm_lb_backend_address_pool_address.test.name
backend_address_pool_id = azurerm_lb_backend_address_pool_address.test.backend_address_pool_id
virtual_network_id = azurerm_lb_backend_address_pool_address.test.virtual_network_id
ip_address = azurerm_lb_backend_address_pool_address.test.ip_address
}
`, template)
}
func (t BackendAddressPoolAddressResourceTests) update(data acceptance.TestData) string {
template := t.template(data)
return fmt.Sprintf(`
provider "azurerm" {
features {}
}
%s
resource "azurerm_lb_backend_address_pool_address" "test" {
name = "address"
backend_address_pool_id = azurerm_lb_backend_address_pool.test.id
virtual_network_id = azurerm_virtual_network.test.id
ip_address = "172.16.31.10"
}
`, template)
}
func (BackendAddressPoolAddressResourceTests) template(data acceptance.TestData) string {
return fmt.Sprintf(`
resource "azurerm_resource_group" "test" {
name = "acctestRG-%d"
location = "%s"
}
resource "azurerm_virtual_network" "test" {
name = "acctestvn-%d"
location = azurerm_resource_group.test.location
resource_group_name = azurerm_resource_group.test.name
address_space = ["192.168.0.0/16"]
}
resource "azurerm_public_ip" "test" {
name = "acctestpip-%d"
location = azurerm_resource_group.test.location
resource_group_name = azurerm_resource_group.test.name
allocation_method = "Static"
sku = "Standard"
}
resource "azurerm_lb" "test" {
name = "acctestlb-%d"
location = azurerm_resource_group.test.location
resource_group_name = azurerm_resource_group.test.name
sku = "Standard"
frontend_ip_configuration {
name = "feip"
public_ip_address_id = azurerm_public_ip.test.id
}
}
resource "azurerm_lb_backend_address_pool" "test" {
name = "internal"
loadbalancer_id = azurerm_lb.test.id
}
`, data.RandomInteger, data.Locations.Primary, data.RandomInteger, data.RandomInteger, data.RandomInteger)
}
|
kamenitxan/Jakon | src/test/scala/core/pagelet/TestJsonPagelet.scala | package core.pagelet
import java.sql.Connection
import core.pagelet.entity.TestJsonPageletData
import cz.kamenitxan.jakon.core.dynamic.entity.JsonFailResponse
import cz.kamenitxan.jakon.core.dynamic.{AbstractJsonPagelet, Get, JsonPagelet, Post}
import spark.{Request, Response}
/**
* Created by TPa on 13.04.2020.
*/
@JsonPagelet(path = "jsonPagelet")
class TestJsonPagelet extends AbstractJsonPagelet {
@Get(path = "/get")
def get(req: Request, res: Response): String = {
"string"
}
@Get(path = "/getResponse")
def getResponse(req: Request, res: Response): JsonFailResponse = {
new JsonFailResponse("some_message")
}
@Get(path = "/throw")
def throwEx(req: Request, res: Response): String = {
throw new IllegalAccessException()
}
@Get(path = "/withDataAndConnection")
def withDataAndConnection(req: Request, res: Response, data: TestJsonPageletData, conn: Connection): String = {
data.msg
}
@Post(path = "/post")
def post(req: Request, res: Response): String = {
"string"
}
@Post(path = "/postNoValidation", validate = false)
def postNoValidation(req: Request, res: Response): String = {
"string"
}
@Post(path = "/postThrow")
def postThrowEx(req: Request, res: Response): String = {
throw new IllegalAccessException()
}
@Post(path = "/postWithDataAndConnection")
def postWithDataAndConnection(req: Request, res: Response, data: TestJsonPageletData, conn: Connection): String = {
data.msg
}
@Post(path = "/postValidate")
def postValidate(req: Request, res: Response, data: TestJsonPageletData): String = {
"validation_ok"
}
}
|
HeyLey/catboost | library/netliba/v12/local_ip_params.cpp | <gh_stars>1000+
#include "stdafx.h"
#include "local_ip_params.h"
namespace NNetliba_v12 {
static ui32 GetIPv6SuffixCrc(const sockaddr_in6& addr) {
TIPv6AddrUnion a;
a.Addr = addr.sin6_addr;
const ui64 suffix = a.Addr64[1];
return (suffix & 0xffffffffll) + (suffix >> 32);
}
ui32 CalcAddressChecksum(const sockaddr_in6& addr) {
Y_ASSERT(addr.sin6_family == AF_INET6);
if (GetIpType(addr) == IPv4) {
TIPv6AddrUnion a;
a.Addr = addr.sin6_addr;
return a.Addr32[3];
} else {
return GetIPv6SuffixCrc(addr);
}
}
static ui32 CalcAddressCrcImpl(const TUdpAddress& addr) {
sockaddr_in6 addr6;
GetWinsockAddr(&addr6, addr);
return CalcAddressChecksum(addr6);
}
ui32 CalcAddressChecksum(const TUdpAddress& addr) {
if (addr.IsIPv4()) {
Y_ASSERT(addr.GetIPv4() == CalcAddressCrcImpl(addr));
return addr.GetIPv4();
}
return CalcAddressCrcImpl(addr);
}
bool TLocalIpParams::Init() {
TVector<TUdpAddress> addrs;
if (!GetLocalAddresses(&addrs))
return false;
for (int i = 0; i < addrs.ysize(); ++i) {
const TUdpAddress& addr = addrs[i];
const ui32 crc = CalcAddressChecksum(addr);
if (addr.IsIPv4()) {
LocalIPListCrcs[IPv4].push_back(crc);
} else {
LocalIPListCrcs[IPv6].push_back(crc);
LocaIPv6List.push_back(TIPv6Addr(addr.Network, addr.Interface));
}
}
return true;
}
bool TLocalIpParams::IsLocal(const TUdpAddress& addr) const {
if (addr.IsIPv4()) {
return IsIn(LocalIPListCrcs[IPv4], addr.GetIPv4());
} else {
return IsIn(LocaIPv6List, TIPv6Addr(addr.Network, addr.Interface));
}
}
}
|
hjki456789/reportBuild | src/main/java/com/jump/utils/property/EnBizEnumProperty.java | package com.jump.utils.property;
import com.google.common.collect.Maps;
import java.util.List;
import java.util.Map;
/**
* @author Jump
* @date 2020/3/9 14:09
*/
public class EnBizEnumProperty extends AbstractBizEnumProperty {
private static Map<String,Map> propertyMap = Maps.newHashMap();
private static Map<String,List<Map<String,String>>> propertiesList = Maps.newHashMap();
@Override
Map<String, Map> getPropertiesMap() {
return propertyMap;
}
@Override
Map<String, List<Map<String, String>>> getPropertiesList() {
return propertiesList;
}
}
|
gavar/google-front-end-web-developer | frontend-apps/wittr/public/js/settings/index.js | <filename>frontend-apps/wittr/public/js/settings/index.js
import TestController from "./TestController";
const settingsForm = document.querySelector(".settings-form");
settingsForm.addEventListener("change", () => {
fetch(settingsForm.action, {
method: settingsForm.method,
body: new FormData(settingsForm),
});
});
if (!self.fetch) {
document.querySelector(".warning").style.display = "block";
}
new TestController(document.querySelector(".tester"));
|
xiaoliable/EssayClassifier | src/tw/edu/ntu/csie/libsvm/model/svm_print_interface.java | <gh_stars>1-10
package tw.edu.ntu.csie.libsvm.model;
public interface svm_print_interface
{
public void print(String s);
}
|
nablarch/nablarch-common-dao | src/main/java/nablarch/common/dao/NamingConversionUtil.java | <reponame>nablarch/nablarch-common-dao<filename>src/main/java/nablarch/common/dao/NamingConversionUtil.java<gh_stars>0
package nablarch.common.dao;
/**
* 変数名やクラス名を相互に変換するユーティリティクラス。
*
* @author kawasima
* @author <NAME>
*/
public final class NamingConversionUtil {
/** 隠蔽コンストラクタ */
private NamingConversionUtil() {
}
/**
* 文字列をアッパーキャメル(パスカルケース)に変換する。
* <p/>
* 例:
* <pre>
* {@code
* NamingConversionUtils.camelize("AAA_BBB_CCC"); -> AaaBbbCcc
* }
* </pre>
*
* @param value 文字列(スネークケースを想定)
* @return 変換後の文字列
*/
public static String camelize(String value) {
if (value == null) {
return null;
}
String[] tokens = value.split("_");
StringBuilder camelized = new StringBuilder(value.length());
for (String token : tokens) {
for (int i = 0; i < token.length(); i++) {
if (i == 0) {
camelized.append(Character.toUpperCase(token.charAt(i)));
} else {
camelized.append(Character.toLowerCase(token.charAt(i)));
}
}
}
return camelized.toString();
}
/**
* アーパーキャメル(パスカルケース)の文字列を全て大文字のスネークケースに変換する。
* <p/>
* 例:
* <pre>
* {@code
* NamingConversionUtils.decamelize("AbcAbcAbc"); -> ABC_ABC_ABC
* }
* </pre>
*
* @param value 文字列(アッパーキャメルを想定)
* @return 変換後の文字列
*/
public static String deCamelize(String value) {
if (value == null) {
return null;
}
StringBuilder deCamelized = new StringBuilder(value.length() + 10);
for (int i = 0; i < value.length(); i++) {
if (Character.isUpperCase(value.charAt(i)) && deCamelized.length() > 0) {
deCamelized.append('_');
}
deCamelized.append(Character.toUpperCase(value.charAt(i)));
}
return deCamelized.toString();
}
}
|
thalida/wordbird | extension/public/app/app.module.js | 'use strict';
angular
.module( 'app', [
require('angular-animate'),
require('angular-resource'),
require('angular-sanitize'),
require('angular-touch'),
require('angular-ui-router'),
require('angular-messages')
])
.config( require('./app.routes.js') );
|
14ms/Minecraft-Disclosed-Source-Modifications | Skizzle/us/myles/viaversion/bukkit/handlers/BukkitDecodeHandler.java | /*
* Decompiled with CFR 0.150.
*
* Could not load the following classes:
* io.netty.buffer.ByteBuf
* io.netty.channel.ChannelHandlerContext
* io.netty.handler.codec.ByteToMessageDecoder
*/
package us.myles.ViaVersion.bukkit.handlers;
import io.netty.buffer.ByteBuf;
import io.netty.channel.ChannelHandlerContext;
import io.netty.handler.codec.ByteToMessageDecoder;
import java.lang.reflect.InvocationTargetException;
import java.util.List;
import us.myles.ViaVersion.api.Via;
import us.myles.ViaVersion.api.data.UserConnection;
import us.myles.ViaVersion.bukkit.util.NMSUtil;
import us.myles.ViaVersion.exception.CancelCodecException;
import us.myles.ViaVersion.exception.CancelDecoderException;
import us.myles.ViaVersion.exception.InformativeException;
import us.myles.ViaVersion.packets.State;
import us.myles.ViaVersion.util.PipelineUtil;
public class BukkitDecodeHandler
extends ByteToMessageDecoder {
private final ByteToMessageDecoder minecraftDecoder;
private final UserConnection info;
public BukkitDecodeHandler(UserConnection info, ByteToMessageDecoder minecraftDecoder) {
this.info = info;
this.minecraftDecoder = minecraftDecoder;
}
/*
* WARNING - Removed try catching itself - possible behaviour change.
*/
protected void decode(ChannelHandlerContext ctx, ByteBuf bytebuf, List<Object> list) throws Exception {
if (!this.info.checkIncomingPacket()) {
bytebuf.clear();
throw CancelDecoderException.generate(null);
}
ByteBuf transformedBuf = null;
try {
if (this.info.shouldTransformPacket()) {
transformedBuf = ctx.alloc().buffer().writeBytes(bytebuf);
this.info.transformIncoming(transformedBuf, CancelDecoderException::generate);
}
try {
list.addAll(PipelineUtil.callDecode(this.minecraftDecoder, ctx, (Object)(transformedBuf == null ? bytebuf : transformedBuf)));
}
catch (InvocationTargetException e) {
if (e.getCause() instanceof Exception) {
throw (Exception)e.getCause();
}
if (e.getCause() instanceof Error) {
throw (Error)e.getCause();
}
}
}
finally {
if (transformedBuf != null) {
transformedBuf.release();
}
}
}
public void exceptionCaught(ChannelHandlerContext ctx, Throwable cause) throws Exception {
if (PipelineUtil.containsCause(cause, CancelCodecException.class)) {
return;
}
super.exceptionCaught(ctx, cause);
if (!NMSUtil.isDebugPropertySet() && PipelineUtil.containsCause(cause, InformativeException.class) && (this.info.getProtocolInfo().getState() != State.HANDSHAKE || Via.getManager().isDebug())) {
cause.printStackTrace();
}
}
}
|
sho25/hive | itests/util/src/main/java/org/apache/hadoop/hive/ql/qoption/QTestAuthorizerHandler.java | begin_unit|revision:0.9.5;language:Java;cregit-version:0.0.1
begin_comment
comment|/* * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */
end_comment
begin_package
package|package
name|org
operator|.
name|apache
operator|.
name|hadoop
operator|.
name|hive
operator|.
name|ql
operator|.
name|qoption
package|;
end_package
begin_import
import|import
name|org
operator|.
name|apache
operator|.
name|hadoop
operator|.
name|hive
operator|.
name|ql
operator|.
name|QTestUtil
import|;
end_import
begin_import
import|import
name|org
operator|.
name|apache
operator|.
name|hadoop
operator|.
name|hive
operator|.
name|ql
operator|.
name|session
operator|.
name|SessionState
import|;
end_import
begin_comment
comment|/** * QTest authorizer option * * Enables authorization for the qtest. * * Example: * --! qt:authorizer */
end_comment
begin_class
specifier|public
class|class
name|QTestAuthorizerHandler
implements|implements
name|QTestOptionHandler
block|{
specifier|private
name|boolean
name|enabled
decl_stmt|;
annotation|@
name|Override
specifier|public
name|void
name|processArguments
parameter_list|(
name|String
name|arguments
parameter_list|)
block|{
name|enabled
operator|=
literal|true
expr_stmt|;
block|}
annotation|@
name|Override
specifier|public
name|void
name|beforeTest
parameter_list|(
name|QTestUtil
name|qt
parameter_list|)
throws|throws
name|Exception
block|{
if|if
condition|(
name|enabled
condition|)
block|{
name|qt
operator|.
name|getConf
argument_list|()
operator|.
name|set
argument_list|(
literal|"hive.test.authz.sstd.hs2.mode"
argument_list|,
literal|"true"
argument_list|)
expr_stmt|;
name|qt
operator|.
name|getConf
argument_list|()
operator|.
name|set
argument_list|(
literal|"hive.security.authorization.manager"
argument_list|,
literal|"org.apache.hadoop.hive.ql.security.authorization.plugin.sqlstd.SQLStdHiveAuthorizerFactoryForTest"
argument_list|)
expr_stmt|;
name|qt
operator|.
name|getConf
argument_list|()
operator|.
name|set
argument_list|(
literal|"hive.security.authenticator.manager"
argument_list|,
literal|"org.apache.hadoop.hive.ql.security.SessionStateConfigUserAuthenticator"
argument_list|)
expr_stmt|;
name|qt
operator|.
name|getConf
argument_list|()
operator|.
name|set
argument_list|(
literal|"hive.security.authorization.enabled"
argument_list|,
literal|"true"
argument_list|)
expr_stmt|;
name|SessionState
operator|.
name|get
argument_list|()
operator|.
name|setAuthenticator
argument_list|(
literal|null
argument_list|)
expr_stmt|;
name|SessionState
operator|.
name|get
argument_list|()
operator|.
name|setAuthorizer
argument_list|(
literal|null
argument_list|)
expr_stmt|;
block|}
block|}
annotation|@
name|Override
specifier|public
name|void
name|afterTest
parameter_list|(
name|QTestUtil
name|qt
parameter_list|)
throws|throws
name|Exception
block|{
name|enabled
operator|=
literal|false
expr_stmt|;
block|}
block|}
end_class
end_unit
|
JurrianFahner/ipf | commons/audit/src/main/java/org/openehealth/ipf/commons/audit/event/AuditMessageBuilder.java | /*
* Copyright 2018 the original author or authors.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.openehealth.ipf.commons.audit.event;
import org.openehealth.ipf.commons.audit.model.AuditMessage;
import org.openehealth.ipf.commons.audit.model.TypeValuePairType;
import org.openehealth.ipf.commons.audit.model.Validateable;
/**
* Base interface for building DICOM audit messages
*
* @author <NAME>
* @since 3.5
*/
public interface AuditMessageBuilder<T extends AuditMessageBuilder<T>> extends Validateable {
/**
* @return the audit message being built
*/
AuditMessage getMessage();
/**
* @return the audit message being built as only element in an array
*/
default AuditMessage[] getMessages() {
return new AuditMessage[]{getMessage()};
}
/**
* Create and set a Type Value Pair instance for a given type and value
*
* @param type the type to set
* @param value the value to set
* @return the Type Value Pair instance
*/
default TypeValuePairType getTypeValuePair(String type, Object value) {
return getTypeValuePair(type, value, null);
}
/**
* Create and set a Type Value Pair instance for a given type and value
*
* @param type the type to set
* @param value the value to set
* @return the Type Value Pair instance
*/
default TypeValuePairType getTypeValuePair(String type, byte[] value) {
return getTypeValuePair(type, value, (byte[])null);
}
/**
* Create and set a Type Value Pair instance for a given type and value
*
* @param type the type to set
* @param value the value to set
* @param defaultValue the value to set if value is null
* @return the Type Value Pair instance
*/
default TypeValuePairType getTypeValuePair(String type, Object value, String defaultValue) {
return new TypeValuePairType(
type,
value != null ? value.toString() : null,
defaultValue);
}
/**
* Create and set a Type Value Pair instance for a given type and value
*
* @param type the type to set
* @param value the value to set
* @param defaultValue the value to set if value is null
* @return the Type Value Pair instance
*/
default TypeValuePairType getTypeValuePair(String type, byte[] value, byte[] defaultValue) {
return new TypeValuePairType(
type,
value != null ? value : null,
defaultValue);
}
/**
* @return this builder
*/
@SuppressWarnings("unchecked")
default T self() {
return (T) this;
}
}
|
Samuel-Rubin621/CS498 | TowerDefense/Intermediate/Plugins/NativizedAssets/Windows/Game/Intermediate/Build/Win64/UE4/Inc/NativizedAssets/Struct_Green__pf3140832796.generated.h | // Copyright Epic Games, Inc. All Rights Reserved.
/*===========================================================================
Generated code exported from UnrealHeaderTool.
DO NOT modify this manually! Edit the corresponding .h files instead!
===========================================================================*/
#include "UObject/ObjectMacros.h"
#include "UObject/ScriptMacros.h"
PRAGMA_DISABLE_DEPRECATION_WARNINGS
#ifdef NATIVIZEDASSETS_Struct_Green__pf3140832796_generated_h
#error "Struct_Green__pf3140832796.generated.h already included, missing '#pragma once' in Struct_Green__pf3140832796.h"
#endif
#define NATIVIZEDASSETS_Struct_Green__pf3140832796_generated_h
#define TowerDefense_Intermediate_Plugins_NativizedAssets_Windows_Game_Source_NativizedAssets_Public_Struct_Green__pf3140832796_h_11_GENERATED_BODY \
friend struct Z_Construct_UScriptStruct_FStruct_Green__pf3140832796_Statics; \
NATIVIZEDASSETS_API static class UScriptStruct* StaticStruct();
template<> NATIVIZEDASSETS_API UScriptStruct* StaticStruct<struct FStruct_Green__pf3140832796>();
#undef CURRENT_FILE_ID
#define CURRENT_FILE_ID TowerDefense_Intermediate_Plugins_NativizedAssets_Windows_Game_Source_NativizedAssets_Public_Struct_Green__pf3140832796_h
PRAGMA_ENABLE_DEPRECATION_WARNINGS
|
qiqingfu/examples-1 | unittest/test/extend/request.test.js | <gh_stars>1000+
'use strict';
const assert = require('assert');
const mock = require('egg-mock');
describe('test/extend/request.test.js', () => {
let app;
before(() => {
app = mock.app();
return app.ready();
});
describe('isChrome()', () => {
it('should true', () => {
const ctx = app.mockContext({
headers: {
'User-Agent': 'Chrome/56.0.2924.51',
},
});
assert(ctx.request.isChrome === true);
});
it('should false', () => {
const ctx = app.mockContext({
headers: {
'User-Agent': 'FireFox/1',
},
});
assert(ctx.request.isChrome === false);
});
});
});
|
bonsaiERP/bonsaiERP | db/migrate/20130702144114_add_tables_updater_id.rb | <reponame>bonsaiERP/bonsaiERP
class AddTablesUpdaterId < ActiveRecord::Migration
def up
PgTools.with_schemas except: 'common' do
add_column :account_ledgers, :updater_id, :integer
add_index :account_ledgers, :updater_id
add_column :accounts, :updater_id, :integer
add_index :accounts, :updater_id
add_column :inventories, :updater_id, :integer
add_index :inventories, :updater_id
end
end
def down
PgTools.with_schemas except: 'common' do
remove_column :account_ledgers, :updater_id
remove_column :accounts, :updater_id
remove_column :inventories, :updater_id
end
end
end
|
quanpands/wflow | pcraster/pcraster-4.2.0/pcraster-4.2.0/source/fern/source/fern/language/io/uncertml2/uncertml2_parser.h | <reponame>quanpands/wflow<gh_stars>0
// -----------------------------------------------------------------------------
// Fern © Geoneric
//
// This file is part of Geoneric Fern which is available under the terms of
// the GNU General Public License (GPL), version 2. If you do not want to
// be bound by the terms of the GPL, you may purchase a proprietary license
// from Geoneric (http://www.geoneric.eu/contact).
// -----------------------------------------------------------------------------
#pragma once
#include <memory>
#include <string>
namespace fern {
class Uncertainty;
//! TODO
/*!
TODO
*/
class UncertML2Parser
{
public:
UncertML2Parser ()=default;
~UncertML2Parser ()=default;
UncertML2Parser (UncertML2Parser&&)=delete;
UncertML2Parser& operator= (UncertML2Parser&&)=delete;
UncertML2Parser (UncertML2Parser const&)=delete;
UncertML2Parser& operator= (UncertML2Parser const&)=delete;
std::shared_ptr<Uncertainty> parse (std::string const& xml) const;
private:
std::shared_ptr<Uncertainty> parse (std::istream& stream) const;
};
} // namespace fern
|
dwws-ufes/2020-UMDb | umdb-app-server/src-gen/main/java/com/ufes/inf/dwws/umdb/persistence/MovieDAOJPA.java | package com.ufes.inf.dwws.umdb.persistence;
import org.springframework.stereotype.Repository;
import javax.persistence.PersistenceContext;
@Repository
public class MovieDAOJPA implements MovieDAOJPA{
@PersistenceContext
EntityManager entityManager;
@Override
public Movie getByID(Long id) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getAllByGenre(Genre genre) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getAllByActor(Actor actor) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getAllByDirector(Director director) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getByName(String name) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getWithReviews(Long id) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getAll() {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie filter(String genre, String director, String actor) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getWithActorsAndGenresAndDirector(Long id) {
// TODO Auto-generated method stub
return null;
}
@Override
public Movie getWithActorsAndGenresAndDirectorAndReviews(Long id) {
// TODO Auto-generated method stub
return null;
}
} |
erdincozden/xs2a | consent-management/consent-xs2a-web/src/main/java/de/adorsys/psd2/consent/web/xs2a/controller/EventController.java | <reponame>erdincozden/xs2a<gh_stars>0
/*
* Copyright 2018-2018 adorsys GmbH & Co KG
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package de.adorsys.psd2.consent.web.xs2a.controller;
import de.adorsys.psd2.consent.api.service.EventServiceEncrypted;
import de.adorsys.psd2.xs2a.core.event.Event;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiResponse;
import io.swagger.annotations.ApiResponses;
import lombok.RequiredArgsConstructor;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
@RestController
@RequiredArgsConstructor
@RequestMapping(path = "api/v1/events")
@Api(value = "api/v1/events", tags = "Events", description = "Provides access to the consent management system for Events")
public class EventController {
private final EventServiceEncrypted eventService;
@PostMapping(path = "/")
@ApiOperation(value = "Creates new event")
@ApiResponses(value = {
@ApiResponse(code = 200, message = "OK"),
@ApiResponse(code = 400, message = "Bad Request")})
public ResponseEntity<Boolean> recordEvent(@RequestBody Event event) {
return new ResponseEntity<>(eventService.recordEvent(event), HttpStatus.OK);
}
}
|
bengarrett/sauce | internal/layout/binarytext_test.go | <reponame>bengarrett/sauce
// This is a raw memory copy of a text mode screen. Also known as a .BIN file.
// This is essentially a collection of character and attribute pairs.
// See http://www.acid.org/info/sauce/sauce.htm#FileType
package layout
import "testing"
func TestBinaryText_String(t *testing.T) {
tests := []struct {
name string
b BinaryText
want string
}{
{"out of range", 999, ""},
{"first and last", 0, "Binary text or a .BIN file"},
}
for _, tt := range tests {
t.Run(tt.name, func(t *testing.T) {
if got := tt.b.String(); got != tt.want {
t.Errorf("BinaryText.String() = %v, want %v", got, tt.want)
}
})
}
}
|
esavard/SoulEVSpy | app/src/main/java/com/evranger/elm327/commands/protocol/can/CANSetProtocolCommand.java | package com.evranger.elm327.commands.protocol.can;
import com.evranger.elm327.commands.AbstractCommand;
/**
* Created by <NAME> <<EMAIL>> on 2015-10-25.
*/
public class CANSetProtocolCommand extends AbstractCommand {
public CANSetProtocolCommand(int protocolNo) {
super("AT SPA" + protocolNo);
}
}
|
acostapazo/event-manager | tests/modules/tasks/create/acceptance/test_post_task.py | import json
import pytest
@pytest.mark.acceptance
def test_should_return_a_200_when_post_task(
client, database, given_any_title, given_any_description
):
headers = {"Content-type": "application/json", "Accept": "text/plain"}
data = {"title": given_any_title, "description": given_any_description}
response = client.post("/taskmanager/task", data=json.dumps(data), headers=headers)
assert response.status_code == 200
assert "task_id" in response.json
assert len(response.json["task_id"]) == 16
assert response.json["message"] == "Created Task"
@pytest.mark.acceptance
def test_should_return_a_405_when_post_task_with_no_data(
client, database, given_any_title, given_any_description
):
headers = {"Content-type": "application/json", "Accept": "text/plain"}
data = {}
response = client.post("/taskmanager/task", data=json.dumps(data), headers=headers)
assert response.status_code == 400
@pytest.mark.acceptance
def test_should_return_a_400_when_post_task_with_no_title(
client, database, given_any_description
):
headers = {"Content-type": "application/json", "Accept": "text/plain"}
data = {"description": given_any_description}
response = client.post("/taskmanager/task", data=json.dumps(data), headers=headers)
assert response.status_code == 400
@pytest.mark.acceptance
def test_should_return_a_400_when_post_task_with_no_description(
client, given_any_title
):
headers = {"Content-type": "application/json", "Accept": "text/plain"}
data = {"title": given_any_title}
response = client.post("/taskmanager/task", data=json.dumps(data), headers=headers)
assert response.status_code == 400
@pytest.mark.acceptance
def test_should_return_a_405_when_post_task_with_title_exceeds_length(
client, given_any_title, given_any_description
):
headers = {"Content-type": "application/json", "Accept": "text/plain"}
data = {"title": given_any_title * 20, "description": given_any_description}
response = client.post("/taskmanager/task", data=json.dumps(data), headers=headers)
assert response.status_code == 405
assert response.json == {
"error": {
"message": "Exceed Length Limit",
"type": "ExceedLengthLimitInputError",
}
}
@pytest.mark.acceptance
def test_should_return_a_405_when_post_task_with_description_exceeds_length(
client, given_any_title, given_any_description
):
headers = {"Content-type": "application/json", "Accept": "text/plain"}
data = {"title": given_any_title, "description": given_any_description * 200}
response = client.post("/taskmanager/task", data=json.dumps(data), headers=headers)
assert response.status_code == 405
assert response.json == {
"error": {
"message": "Exceed Length Limit",
"type": "ExceedLengthLimitInputError",
}
}
|
lastweek/source-freebsd | src/sys/mips/atheros/ar531x/ar5312_chip.c | <gh_stars>0
/*-
* Copyright (c) 2016 <NAME>
* Copyright (c) 2010 <NAME>
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
* OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
*/
#include <sys/cdefs.h>
__FBSDID("$FreeBSD$");
#include "opt_ddb.h"
#include <sys/param.h>
#include <sys/conf.h>
#include <sys/kernel.h>
#include <sys/socket.h>
#include <sys/systm.h>
#include <sys/bus.h>
#include <sys/cons.h>
#include <sys/kdb.h>
#include <sys/reboot.h>
#include <vm/vm.h>
#include <vm/vm_page.h>
#include <net/ethernet.h>
#include <machine/clock.h>
#include <machine/cpu.h>
#include <machine/cpuregs.h>
#include <machine/hwfunc.h>
#include <machine/md_var.h>
#include <machine/trap.h>
#include <machine/vmparam.h>
#include <mips/atheros/ar531x/ar5312reg.h>
#include <mips/atheros/ar531x/ar5315reg.h>
#include <mips/atheros/ar531x/ar5315_cpudef.h>
#include <mips/atheros/ar531x/ar5315_setup.h>
static void
ar5312_chip_detect_mem_size(void)
{
uint32_t memsize;
uint32_t memcfg, bank0, bank1;
/*
* Determine the memory size as established by system
* firmware.
*
* NB: we allow compile time override
*/
memcfg = ATH_READ_REG(AR5312_SDRAMCTL_BASE + AR5312_SDRAMCTL_MEM_CFG1);
bank0 = __SHIFTOUT(memcfg, AR5312_MEM_CFG1_BANK0);
bank1 = __SHIFTOUT(memcfg, AR5312_MEM_CFG1_BANK1);
memsize = (bank0 ? (1 << (bank0 + 1)) : 0) +
(bank1 ? (1 << (bank1 + 1)) : 0);
memsize <<= 20;
realmem = memsize;
}
static void
ar5312_chip_detect_sys_frequency(void)
{
uint32_t predivisor;
uint32_t multiplier;
const uint32_t clockctl = ATH_READ_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_CLOCKCTL);
if(ar531x_soc == AR531X_SOC_AR5313) {
predivisor = __SHIFTOUT(clockctl, AR2313_CLOCKCTL_PREDIVIDE);
multiplier = __SHIFTOUT(clockctl, AR2313_CLOCKCTL_MULTIPLIER);
} else {
predivisor = __SHIFTOUT(clockctl, AR5312_CLOCKCTL_PREDIVIDE);
multiplier = __SHIFTOUT(clockctl, AR5312_CLOCKCTL_MULTIPLIER);
}
const uint32_t divisor = (0x5421 >> (predivisor * 4)) & 15;
const uint32_t cpufreq = (40000000 / divisor) * multiplier;
u_ar531x_cpu_freq = cpufreq;
u_ar531x_ahb_freq = cpufreq / 4;
u_ar531x_ddr_freq = 0;
}
/*
* This does not lock the CPU whilst doing the work!
*/
static void
ar5312_chip_device_reset(void)
{
ATH_WRITE_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_RESETCTL,
AR5312_RESET_SYSTEM);
}
static void
ar5312_chip_device_start(void)
{
uint32_t cfg0, cfg1;
uint32_t bank0, bank1;
uint32_t size0, size1;
cfg0 = ATH_READ_REG(AR5312_SDRAMCTL_BASE + AR5312_SDRAMCTL_MEM_CFG0);
cfg1 = ATH_READ_REG(AR5312_SDRAMCTL_BASE + AR5312_SDRAMCTL_MEM_CFG1);
bank0 = __SHIFTOUT(cfg1, AR5312_MEM_CFG1_BANK0);
bank1 = __SHIFTOUT(cfg1, AR5312_MEM_CFG1_BANK1);
size0 = bank0 ? (1 << (bank0 + 1)) : 0;
size1 = bank1 ? (1 << (bank1 + 1)) : 0;
size0 <<= 20;
size1 <<= 20;
printf("SDRMCTL %x %x %x %x\n", cfg0, cfg1, size0, size1);
ATH_READ_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_AHBPERR);
ATH_READ_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_AHBDMAE);
// ATH_WRITE_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_WDOG_CTL, 0);
ATH_WRITE_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_ENABLE, 0);
ATH_WRITE_REG(AR5312_SYSREG_BASE+AR5312_SYSREG_ENABLE,
ATH_READ_REG(AR5312_SYSREG_BASE+AR5312_SYSREG_ENABLE) |
AR5312_ENABLE_ENET0 | AR5312_ENABLE_ENET1);
}
static int
ar5312_chip_device_stopped(uint32_t mask)
{
uint32_t reg;
reg = ATH_READ_REG(AR5312_SYSREG_BASE + AR5312_SYSREG_RESETCTL);
return ((reg & mask) == mask);
}
static void
ar5312_chip_set_mii_speed(uint32_t unit, uint32_t speed)
{
}
/* Speed is either 10, 100 or 1000 */
static void
ar5312_chip_set_pll_ge(int unit, int speed)
{
}
static void
ar5312_chip_ddr_flush_ge(int unit)
{
}
static void
ar5312_chip_soc_init(void)
{
u_ar531x_uart_addr = MIPS_PHYS_TO_KSEG1(AR5312_UART0_BASE);
u_ar531x_gpio_di = AR5312_GPIO_DI;
u_ar531x_gpio_do = AR5312_GPIO_DO;
u_ar531x_gpio_cr = AR5312_GPIO_CR;
u_ar531x_gpio_pins = AR5312_GPIO_PINS;
u_ar531x_wdog_ctl = AR5312_SYSREG_WDOG_CTL;
u_ar531x_wdog_timer = AR5312_SYSREG_WDOG_TIMER;
}
static uint32_t
ar5312_chip_get_eth_pll(unsigned int mac, int speed)
{
return 0;
}
struct ar5315_cpu_def ar5312_chip_def = {
&ar5312_chip_detect_mem_size,
&ar5312_chip_detect_sys_frequency,
&ar5312_chip_device_reset,
&ar5312_chip_device_start,
&ar5312_chip_device_stopped,
&ar5312_chip_set_pll_ge,
&ar5312_chip_set_mii_speed,
&ar5312_chip_ddr_flush_ge,
&ar5312_chip_get_eth_pll,
&ar5312_chip_soc_init,
};
|
khangaikhuu-mstars/mstars-exercises | Baatarkhuu/Async programming/11.29/Exercise-01/app.js | <gh_stars>0
// const myPromise = new Promise((resolve, reject) => {
// const xhr = new XMLHttpRequest();
// xhr.open("GET", "sidebar.html");
// xhr.onreadystatechange = function () {
// if (!xhr.status == 200) {
// document.getElementById("ajax").innerHTML = xhr.responseText;
// return resolve("It is working");
// }else {
// return reject('Reject is working');
// }
// };
// xhr.send();
// });
// myPromise.then((data) => {
// console.log(data)
// }).catch((error) => console.log(error))
// console.log(myPromise);
const btn = document.getElementById("button")
const myPromise = new Promise((resolve, reject) => {
const xhr = new XMLHttpRequest();
xhr.open("GET", "sidebar.html");
xhr.onreadystatechange = function () {
if (xhr.status == 200) {
return resolve("It is working");
}else {
return reject('Not found');
}
};
xhr.send();
});
myPromise.then((data) => {
document.getElementById('ajax').innerHTML = `<div><h1>${data}<h1></div>`
}).catch((error) => document.getElementById("ajax").innerHTML = `<div><h1>${error}<h1></div>`)
.finally(() => {btn.style.display = "none"});
|
larsbratholm/champs_kaggle | solutions/12/src/cormorant/tests/cormorant_tests.py | import torch
from torch.utils.data import DataLoader
import logging
from cormorant.cg_lib import rotations as rot
from cormorant.data import collate_fn
def _gen_rot(data, angles, maxl):
alpha, beta, gamma = angles
D = rot.WignerD_list(maxl, alpha, beta, gamma)
R = rot.EulerRot(alpha, beta, gamma)
return D, R
def covariance_test(model, data):
logging.info('Beginning covariance test!')
targets_rotout, outputs_rotin = [], []
angles = torch.rand(3)
D, R = _gen_rot(data, angles, max(model.maxl))
data_rotout = data
data_rotin = {key: val.clone() if type(val) is torch.Tensor else None for key, val in data.items()}
data_rotin['positions'] = rot.rotate_cart_vec(R, data_rotin['positions'])
outputs_rotout, reps_rotout, _ = model(data_rotout, covariance_test=True)
outputs_rotin, reps_rotin, _ = model(data_rotin, covariance_test=True)
reps_rotout, reps_rotin = reps_rotout[0], reps_rotin[0]
invariance_test = (outputs_rotout - outputs_rotin).norm()
reps_rotout = [rot.rotate_rep(D, reps) for reps in reps_rotout]
covariance_test_norm = [[(part_in - part_out).norm().item() for (part_in, part_out) in zip(level_in, level_out)] for (level_in, level_out) in zip(reps_rotin, reps_rotout)]
covariance_test_mean = [[(part_in - part_out).abs().mean().item() for (part_in, part_out) in zip(level_in, level_out)] for (level_in, level_out) in zip(reps_rotin, reps_rotout)]
covariance_test_max = torch.cat([torch.tensor([(part_in - part_out).abs().max().item() for (part_in, part_out) in zip(level_in, level_out)]) for (level_in, level_out) in zip(reps_rotin, reps_rotout)])
covariance_test_max = covariance_test_max.max().item()
if set([len(part) for part in reps_rotout]) == 1:
covariance_test_norm = torch.tensor(covariance_test_norm)
covariance_test_mean = torch.tensor(covariance_test_mean)
else:
covariance_test_norm = [torch.tensor(p) for p in covariance_test_norm]
covariance_test_mean = [torch.tensor(p) for p in covariance_test_mean]
logging.info('Rotation Invariance test: {:0.5g}'.format(invariance_test))
logging.info('Largest deviation in covariance test : {:0.5g}'.format(covariance_test_max))
# If the largest deviation in the covariance test is greater than 1e-5,
# display l1 and l2 norms of each irrep along each level.
if covariance_test_max > 1e-5:
logging.warning('Largest deviation in covariance test {:0.5g} detected! Detailed summary:'.format(covariance_test_max))
for lvl_idx, (lvl_norm, lvl_mean) in enumerate(zip(covariance_test_norm, covariance_test_mean)):
for ell_idx, (ell_norm, ell_mean) in enumerate(zip(lvl_norm, lvl_mean)):
logging.warning('(lvl, ell) = ({}, {}) -> {:0.5g} (mean) {:0.5g} (max)'.format(lvl_idx, ell_idx, ell_norm, ell_mean))
def permutation_test(model, data):
logging.info('Beginning permutation test!')
mask = data['atom_mask']
# Generate a list of indices for each molecule.
# We will generate a permutation only for the atoms that exist (are not masked.)
perm = 1*torch.arange(mask.shape[1]).expand(mask.shape[0], -1)
for idx in range(mask.shape[0]):
num_atoms = (mask[idx, :].long()).sum()
perm[idx, :num_atoms] = torch.randperm(num_atoms)
apply_perm = lambda mat: torch.stack([mat[idx, p] for (idx, p) in enumerate(perm)])
assert((mask == apply_perm(mask)).all())
data_noperm = data
data_perm = {key: apply_perm(val) if torch.is_tensor(val) and val.dim() > 1 else val for key, val in data.items()}
outputs_perm = model(data_perm)
outputs_noperm = model(data_noperm)
invariance_test = (outputs_perm - outputs_noperm).abs().max()
logging.info('Permutation Invariance test: {}'.format(invariance_test))
def batch_test(model, data):
logging.info('Beginning batch invariance test!')
data_split = {key: val.unbind(dim=0) if (torch.is_tensor(val) and val.numel() > 1) else val for key, val in data.items()}
data_split = [{key: val[idx].unsqueeze(0) if type(val) is tuple else val for key, val in data_split.items()} for idx in range(len(data['charges']))]
outputs_split = torch.cat([model(data_sub) for data_sub in data_split])
outputs_full = model(data)
invariance_test = (outputs_split - outputs_full).abs().max()
logging.info('Batch invariance test: {}'.format(invariance_test))
def cormorant_tests(model, dataloader, args, tests=['covariance'], charge_scale=1):
if not args.test:
logging.info("WARNING: network tests disabled!")
return
logging.info("Testing network for symmetries:")
model.eval()
charge_power, num_species = model.charge_power, model.num_species
data = next(iter(dataloader))
covariance_test(model, data)
permutation_test(model, data)
batch_test(model, data)
logging.info('Test complete!')
|
Emersonxuelinux/aliyun-odps-python-sdk | odps/models/tests/test_partitions.py | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 1999-2017 Alibaba Group Holding Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from datetime import datetime
from odps.tests.core import TestBase, tn
from odps.compat import unittest
from odps.models import Schema
from odps import types
class Test(TestBase):
def testPartitions(self):
test_table_name = tn('pyodps_t_tmp_partitions_table')
partitions = ['s=%s' % i for i in range(3)]
schema = Schema.from_lists(['id', ], ['string', ], ['s', ], ['string', ])
self.odps.delete_table(test_table_name, if_exists=True)
table = self.odps.create_table(test_table_name, schema)
for partition in partitions:
table.create_partition(partition)
self.assertEqual(sorted([str(types.PartitionSpec(p)) for p in partitions]),
sorted([str(p.partition_spec) for p in table.partitions]))
table.get_partition(partitions[0]).drop()
self.assertEqual(sorted([str(types.PartitionSpec(p)) for p in partitions[1:]]),
sorted([str(p.partition_spec) for p in table.partitions]))
p = next(table.partitions)
self.assertGreater(len(p.columns), 0)
p.reload()
self.assertGreater(len(p.columns), 0)
self.odps.delete_table(test_table_name)
def testSubPartitions(self):
test_table_name = tn('pyodps_t_tmp_sub_partitions_table')
root_partition = 'type=test'
sub_partitions = ['s=%s' % i for i in range(3)]
schema = Schema.from_lists(['id', ], ['string', ], ['type', 's'], ['string', 'string'])
self.odps.delete_table(test_table_name, if_exists=True)
table = self.odps.create_table(test_table_name, schema)
partitions = [root_partition+','+p for p in sub_partitions]
partitions.append('type=test2,s=0')
for partition in partitions:
table.create_partition(partition)
self.assertEqual(sorted([str(types.PartitionSpec(p)) for p in partitions]),
sorted([str(p.partition_spec) for p in table.partitions]))
self.assertEqual(len(list(table.iterate_partitions(root_partition))), 3)
table.delete_partition(partitions[0])
self.assertEqual(sorted([str(types.PartitionSpec(p)) for p in partitions[1:]]),
sorted([str(p.partition_spec) for p in table.partitions]))
self.odps.delete_table(test_table_name)
def testPartition(self):
test_table_name = tn('pyodps_t_tmp_partition_table')
partition = 's=1'
schema = Schema.from_lists(['id', ], ['string', ], ['s', ], ['string', ])
self.odps.delete_table(test_table_name, if_exists=True)
table = self.odps.create_table(test_table_name, schema)
partition = table.create_partition(partition)
self.assertFalse(partition._getattr('_is_extend_info_loaded'))
self.assertFalse(partition._getattr('_loaded'))
self.assertIsNone(partition._getattr('creation_time'))
self.assertIsNone(partition._getattr('last_meta_modified_time'))
self.assertIsNone(partition._getattr('last_modified_time'))
self.assertIsNone(partition._getattr('size'))
self.assertIsNone(partition._getattr('is_archived'))
self.assertIsNone(partition._getattr('is_exstore'))
self.assertIsNone(partition._getattr('lifecycle'))
self.assertIsNone(partition._getattr('physical_size'))
self.assertIsNone(partition._getattr('file_num'))
self.assertIsInstance(partition.is_archived, bool)
self.assertIsInstance(partition.is_exstore, bool)
self.assertIsInstance(partition.lifecycle, int)
self.assertIsInstance(partition.physical_size, int)
self.assertIsInstance(partition.file_num, int)
self.assertIsInstance(partition.creation_time, datetime)
self.assertIsInstance(partition.last_meta_modified_time, datetime)
self.assertIsInstance(partition.last_modified_time, datetime)
self.assertIsInstance(partition.size, int)
self.assertTrue(partition._is_extend_info_loaded)
self.assertTrue(partition.is_loaded)
self.assertTrue(table.exist_partition(partition))
self.assertFalse(table.exist_partition('s=a_non_exist_partition'))
self.odps.delete_table(test_table_name)
self.assertFalse(table.exist_partition(partition))
if __name__ == '__main__':
unittest.main() |
jiusandeerduo/alumni-database-platform | cloudfunctions/cloud/project/controller/admin/admin_order_controller.js | /**
* Notes: 资讯模块后台管理-控制器
* Ver : CCMiniCloud Framework 2.0.1 ALL RIGHTS RESERVED BY <EMAIL>
* Date: 2021-07-11 10:20:00
*/
const BaseAdminController = require('./base_admin_controller.js');
const AdminOrderService = require('../../service/admin/admin_order_service.js');
const timeUtil = require('../../../framework/utils/time_util.js');
const dataUtil = require('../../../framework/utils/data_util.js');
const contentCheck = require('../../../framework/validate/content_check.js');
class AdminOrderController extends BaseAdminController {
/**
* 退款
*/
async refund() {
await this.isAdmin();
// 数据校验
let rules = {
id: 'must|id',
};
// 取得数据
let input = this.validateData(rules);
let service = new AdminOrderService();
await service.refund(input.id);
}
/** 资讯列表 */
async getOrderList() {
await this.isAdmin();
// 数据校验
let rules = {
search: 'string|min:1|max:30|name=搜索条件',
sortType: 'string|name=搜索类型',
sortVal: 'name=搜索类型值',
orderBy: 'object|name=排序',
whereEx: 'object|name=附加查询条件',
page: 'must|int|default=1',
size: 'int',
isTotal: 'bool',
oldTotal: 'int',
};
// 取得数据
let input = this.validateData(rules);
let service = new AdminOrderService();
let result = await service.getOrderList(input);
// 数据格式化
let list = result.list;
for (let k in list) {
list[k].ORDER_ADD_TIME = timeUtil.timestamp2Time(list[k].ORDER_ADD_TIME);
list[k].ORDER_REFUND_TIME = timeUtil.timestamp2Time(list[k].ORDER_REFUND_TIME);
}
result.list = list;
return result;
}
/************** 数据导出 BEGIN ********************* */
// 当前是否有导出文件生成
async orderDataGet() {
await this.isAdmin();
// 数据校验
let rules = {};
// 取得数据
let input = this.validateData(rules);
let service = new AdminOrderService();
return await service.getOrderDataURL();
}
// 导出数据
async orderDataExport() {
await this.isAdmin();
// 数据校验
let rules = {
condition: 'string|name=导出条件',
};
// 取得数据
let input = this.validateData(rules);
let service = new AdminOrderService();
return await service.exportOrderDataExcel(input.condition);
}
// 删除导出的订单数据
async orderDataDel() {
await this.isAdmin();
// 数据校验
let rules = {};
// 取得数据
let input = this.validateData(rules);
let service = new AdminOrderService();
return await service.deleteOrderDataExcel();
}
/************** 数据导出 END ********************* */
}
module.exports = AdminOrderController; |
multei/web | src/services/healthcheck.js | import Api from "../api"
export const getHealthCheckResponse = () => Api().get("/health-check")
|
subutai-io/subutai | management/server/subutai-common/src/main/java/io/subutai/common/peer/PeerNotRegisteredException.java | package io.subutai.common.peer;
public class PeerNotRegisteredException extends PeerException
{
public PeerNotRegisteredException()
{
}
public PeerNotRegisteredException( final String message )
{
super( message );
}
}
|
jingshuai5213/bus | bus-core/src/main/java/org/aoju/bus/core/toolkit/NameKit.java | /*********************************************************************************
* *
* The MIT License (MIT) *
* *
* Copyright (c) 2015-2020 aoju.org and other contributors. *
* *
* Permission is hereby granted, free of charge, to any person obtaining a copy *
* of this software and associated documentation files (the "Software"), to deal *
* in the Software without restriction, including without limitation the rights *
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell *
* copies of the Software, and to permit persons to whom the Software is *
* furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE *
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER *
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, *
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN *
* THE SOFTWARE. *
********************************************************************************/
package org.aoju.bus.core.toolkit;
import java.util.ArrayList;
import java.util.List;
/**
* 生成姓名
*
* @author <NAME>
* @version 6.0.1
* @since JDK 1.8+
*/
public class NameKit {
private static List<String> EN_FIRST_LIST = new ArrayList<>();
private static List<String> EN_LAST_LIST = new ArrayList<>();
private static List<String> CN_LAST_NAME = new ArrayList<>();
private static List<String> CN_FIRST_NAME = new ArrayList<>();
static {
initEN_FIRST_LIST();
initEN_LAST_LIST();
initCN_LAST_NAME();
initCN_FIRST_NAME();
}
public static String getEnName() {
String head = EN_FIRST_LIST.get((int) (Math.random() * EN_FIRST_LIST.size()));
String tail = EN_LAST_LIST.get((int) (Math.random() * EN_LAST_LIST.size()));
return head + tail;
}
public static String getCnName() {
String head = CN_LAST_NAME.get((int) (Math.random() * CN_LAST_NAME.size()));
String tail = CN_FIRST_NAME.get((int) (Math.random() * CN_FIRST_NAME.size()));
return head + tail;
}
public static void initEN_FIRST_LIST() {
EN_FIRST_LIST.add("Ter");
EN_FIRST_LIST.add("Wind");
EN_FIRST_LIST.add("Buck");
EN_FIRST_LIST.add("Glo");
EN_FIRST_LIST.add("Ray");
EN_FIRST_LIST.add("Black");
EN_FIRST_LIST.add("Bright");
EN_FIRST_LIST.add("Claire");
EN_FIRST_LIST.add("Blithe");
EN_FIRST_LIST.add("O'Ca");
EN_FIRST_LIST.add("Rams");
EN_FIRST_LIST.add("Dawn");
EN_FIRST_LIST.add("Kirk");
EN_FIRST_LIST.add("Beck");
EN_FIRST_LIST.add("Mill");
EN_FIRST_LIST.add("Hob");
EN_FIRST_LIST.add("Hod");
EN_FIRST_LIST.add("Fitch");
EN_FIRST_LIST.add("Wins");
EN_FIRST_LIST.add("Gals");
EN_FIRST_LIST.add("Boyd");
EN_FIRST_LIST.add("Myr");
EN_FIRST_LIST.add("Tours");
EN_FIRST_LIST.add("Hoo");
EN_FIRST_LIST.add("Dave");
EN_FIRST_LIST.add("Steele");
EN_FIRST_LIST.add("Ruth");
EN_FIRST_LIST.add("Brian");
EN_FIRST_LIST.add("Dier");
EN_FIRST_LIST.add("Mike");
EN_FIRST_LIST.add("Hoy");
EN_FIRST_LIST.add("Piers");
EN_FIRST_LIST.add("Lind");
EN_FIRST_LIST.add("Bill");
EN_FIRST_LIST.add("Booth");
EN_FIRST_LIST.add("A");
EN_FIRST_LIST.add("Ab");
EN_FIRST_LIST.add("Ser");
EN_FIRST_LIST.add("June");
EN_FIRST_LIST.add("Ac");
EN_FIRST_LIST.add("B");
EN_FIRST_LIST.add("Ad");
EN_FIRST_LIST.add("E");
EN_FIRST_LIST.add("F");
EN_FIRST_LIST.add("Brews");
EN_FIRST_LIST.add("Ag");
EN_FIRST_LIST.add("Chil");
EN_FIRST_LIST.add("Flo");
EN_FIRST_LIST.add("I");
EN_FIRST_LIST.add("Elroy");
EN_FIRST_LIST.add("Al");
EN_FIRST_LIST.add("L");
EN_FIRST_LIST.add("Tha");
EN_FIRST_LIST.add("An");
EN_FIRST_LIST.add("Paul");
EN_FIRST_LIST.add("O");
EN_FIRST_LIST.add("Beer");
EN_FIRST_LIST.add("Hutt");
EN_FIRST_LIST.add("The");
EN_FIRST_LIST.add("Ar");
EN_FIRST_LIST.add("Leif");
EN_FIRST_LIST.add("As");
EN_FIRST_LIST.add("Baird");
EN_FIRST_LIST.add("S");
EN_FIRST_LIST.add("At");
EN_FIRST_LIST.add("Au");
EN_FIRST_LIST.add("U");
EN_FIRST_LIST.add("Stra");
EN_FIRST_LIST.add("Jud");
EN_FIRST_LIST.add("Tho");
EN_FIRST_LIST.add("Dia");
EN_FIRST_LIST.add("Doug");
EN_FIRST_LIST.add("God");
EN_FIRST_LIST.add("Fast");
EN_FIRST_LIST.add("Ba");
EN_FIRST_LIST.add("Bea");
EN_FIRST_LIST.add("Lyn");
EN_FIRST_LIST.add("Walsh");
EN_FIRST_LIST.add("Be");
EN_FIRST_LIST.add("Dil");
EN_FIRST_LIST.add("Lyt");
EN_FIRST_LIST.add("Bi");
EN_FIRST_LIST.add("Bel");
EN_FIRST_LIST.add("Scrip");
EN_FIRST_LIST.add("Jus");
EN_FIRST_LIST.add("Ben");
EN_FIRST_LIST.add("Gos");
EN_FIRST_LIST.add("Gor");
EN_FIRST_LIST.add("Bo");
EN_FIRST_LIST.add("Hicks");
EN_FIRST_LIST.add("Ber");
EN_FIRST_LIST.add("Tris");
EN_FIRST_LIST.add("Bet");
EN_FIRST_LIST.add("Tif");
EN_FIRST_LIST.add("Hale");
EN_FIRST_LIST.add("Bes");
EN_FIRST_LIST.add("Joan");
EN_FIRST_LIST.add("Pad");
EN_FIRST_LIST.add("Bu");
EN_FIRST_LIST.add("Hearst");
EN_FIRST_LIST.add("Wol");
EN_FIRST_LIST.add("Reg");
EN_FIRST_LIST.add("Woo");
EN_FIRST_LIST.add("By");
EN_FIRST_LIST.add("Pag");
EN_FIRST_LIST.add("Tim");
EN_FIRST_LIST.add("Pal");
EN_FIRST_LIST.add("Crich");
EN_FIRST_LIST.add("Todd");
EN_FIRST_LIST.add("Pan");
EN_FIRST_LIST.add("Cha");
EN_FIRST_LIST.add("Sibyl");
EN_FIRST_LIST.add("Ca");
EN_FIRST_LIST.add("Bing");
EN_FIRST_LIST.add("Par");
EN_FIRST_LIST.add("Yves");
EN_FIRST_LIST.add("Bran");
EN_FIRST_LIST.add("Ce");
EN_FIRST_LIST.add("Ade");
EN_FIRST_LIST.add("Rex");
EN_FIRST_LIST.add("Pau");
EN_FIRST_LIST.add("Rey");
EN_FIRST_LIST.add("Pay");
EN_FIRST_LIST.add("Co");
EN_FIRST_LIST.add("Brad");
EN_FIRST_LIST.add("Sha");
EN_FIRST_LIST.add("Stone");
EN_FIRST_LIST.add("She");
EN_FIRST_LIST.add("Need");
EN_FIRST_LIST.add("Cu");
EN_FIRST_LIST.add("Cy");
EN_FIRST_LIST.add("Tess");
EN_FIRST_LIST.add("North");
EN_FIRST_LIST.add("Da");
EN_FIRST_LIST.add("Christ");
EN_FIRST_LIST.add("Frances");
EN_FIRST_LIST.add("De");
EN_FIRST_LIST.add("Gold");
EN_FIRST_LIST.add("Di");
EN_FIRST_LIST.add("Oisen");
EN_FIRST_LIST.add("Do");
EN_FIRST_LIST.add("Cis");
EN_FIRST_LIST.add("Fox");
EN_FIRST_LIST.add("Dean");
EN_FIRST_LIST.add("Fow");
EN_FIRST_LIST.add("Sid");
EN_FIRST_LIST.add("Sig");
EN_FIRST_LIST.add("Brooke");
EN_FIRST_LIST.add("Du");
EN_FIRST_LIST.add("Dy");
EN_FIRST_LIST.add("Samp");
EN_FIRST_LIST.add("Gra");
EN_FIRST_LIST.add("Sin");
EN_FIRST_LIST.add("Gre");
EN_FIRST_LIST.add("Smed");
EN_FIRST_LIST.add("Ed");
EN_FIRST_LIST.add("Gri");
EN_FIRST_LIST.add("Ef");
EN_FIRST_LIST.add("Eg");
EN_FIRST_LIST.add("Ei");
EN_FIRST_LIST.add("Gro");
EN_FIRST_LIST.add("O'Con");
EN_FIRST_LIST.add("Bird");
EN_FIRST_LIST.add("El");
EN_FIRST_LIST.add("Em");
EN_FIRST_LIST.add("Fors");
EN_FIRST_LIST.add("Er");
EN_FIRST_LIST.add("Holt");
EN_FIRST_LIST.add("Es");
EN_FIRST_LIST.add("Woolf");
EN_FIRST_LIST.add("Eu");
EN_FIRST_LIST.add("Field");
EN_FIRST_LIST.add("Kris");
EN_FIRST_LIST.add("Hub");
EN_FIRST_LIST.add("Hud");
EN_FIRST_LIST.add("Crai");
EN_FIRST_LIST.add("Rho");
EN_FIRST_LIST.add("Boyce");
EN_FIRST_LIST.add("Fa");
EN_FIRST_LIST.add("Hug");
EN_FIRST_LIST.add("Hul");
EN_FIRST_LIST.add("Fe");
EN_FIRST_LIST.add("Hun");
EN_FIRST_LIST.add("Lynch");
EN_FIRST_LIST.add("Grant");
EN_FIRST_LIST.add("Hum");
EN_FIRST_LIST.add("Young");
EN_FIRST_LIST.add("Kent");
EN_FIRST_LIST.add("Bil");
EN_FIRST_LIST.add("Fo");
EN_FIRST_LIST.add("Bir");
EN_FIRST_LIST.add("Hux");
EN_FIRST_LIST.add("Pea");
EN_FIRST_LIST.add("Joel");
EN_FIRST_LIST.add("Peg");
EN_FIRST_LIST.add("White");
EN_FIRST_LIST.add("Fre");
EN_FIRST_LIST.add("Pen");
EN_FIRST_LIST.add("Cla");
EN_FIRST_LIST.add("Ga");
EN_FIRST_LIST.add("Ford");
EN_FIRST_LIST.add("Nan");
EN_FIRST_LIST.add("Per");
EN_FIRST_LIST.add("Cle");
EN_FIRST_LIST.add("Ge");
EN_FIRST_LIST.add("Pet");
EN_FIRST_LIST.add("Nat");
EN_FIRST_LIST.add("John");
EN_FIRST_LIST.add("Crane");
EN_FIRST_LIST.add("Cly");
EN_FIRST_LIST.add("Ode");
EN_FIRST_LIST.add("Browne");
EN_FIRST_LIST.add("Dob");
EN_FIRST_LIST.add("Back");
EN_FIRST_LIST.add("Kerr");
EN_FIRST_LIST.add("Ha");
EN_FIRST_LIST.add("Bach");
EN_FIRST_LIST.add("He");
EN_FIRST_LIST.add("Phil");
EN_FIRST_LIST.add("Hood");
EN_FIRST_LIST.add("Neil");
EN_FIRST_LIST.add("Ever");
EN_FIRST_LIST.add("Dol");
EN_FIRST_LIST.add("Hi");
EN_FIRST_LIST.add("Gun");
EN_FIRST_LIST.add("Don");
EN_FIRST_LIST.add("Pear");
EN_FIRST_LIST.add("Gus");
EN_FIRST_LIST.add("Ho");
EN_FIRST_LIST.add("Guy");
EN_FIRST_LIST.add("Dou");
EN_FIRST_LIST.add("Hu");
EN_FIRST_LIST.add("Mac");
EN_FIRST_LIST.add("Troy");
EN_FIRST_LIST.add("Mab");
EN_FIRST_LIST.add("Doy");
EN_FIRST_LIST.add("Hy");
EN_FIRST_LIST.add("Mag");
EN_FIRST_LIST.add("Tom");
EN_FIRST_LIST.add("Morse");
EN_FIRST_LIST.add("Bla");
EN_FIRST_LIST.add("Mal");
EN_FIRST_LIST.add("Hart");
EN_FIRST_LIST.add("Swift");
EN_FIRST_LIST.add("Man");
EN_FIRST_LIST.add("Bell");
EN_FIRST_LIST.add("Mar");
EN_FIRST_LIST.add("Mau");
EN_FIRST_LIST.add("Wilde");
EN_FIRST_LIST.add("Mat");
EN_FIRST_LIST.add("May");
EN_FIRST_LIST.add("In");
EN_FIRST_LIST.add("Max");
EN_FIRST_LIST.add("Ir");
EN_FIRST_LIST.add("Shaw");
EN_FIRST_LIST.add("Beard");
EN_FIRST_LIST.add("Bly");
EN_FIRST_LIST.add("Phi");
EN_FIRST_LIST.add("Ja");
EN_FIRST_LIST.add("Je");
EN_FIRST_LIST.add("Cof");
EN_FIRST_LIST.add("Wyatt");
EN_FIRST_LIST.add("Com");
EN_FIRST_LIST.add("Col");
EN_FIRST_LIST.add("Coo");
EN_FIRST_LIST.add("Con");
EN_FIRST_LIST.add("James");
EN_FIRST_LIST.add("Jo");
EN_FIRST_LIST.add("Cop");
EN_FIRST_LIST.add("Cor");
EN_FIRST_LIST.add("Cot");
EN_FIRST_LIST.add("Cow");
EN_FIRST_LIST.add("Ju");
EN_FIRST_LIST.add("Croft");
EN_FIRST_LIST.add("Jane");
EN_FIRST_LIST.add("Son");
EN_FIRST_LIST.add("Nel");
EN_FIRST_LIST.add("Ka");
EN_FIRST_LIST.add("Lan");
EN_FIRST_LIST.add("Sou");
EN_FIRST_LIST.add("Lam");
EN_FIRST_LIST.add("Pit");
EN_FIRST_LIST.add("Ke");
EN_FIRST_LIST.add("Lar");
EN_FIRST_LIST.add("Frank");
EN_FIRST_LIST.add("Lat");
EN_FIRST_LIST.add("New");
EN_FIRST_LIST.add("Lau");
EN_FIRST_LIST.add("Horn");
EN_FIRST_LIST.add("Tra");
EN_FIRST_LIST.add("Law");
EN_FIRST_LIST.add("Snow");
EN_FIRST_LIST.add("Tre");
EN_FIRST_LIST.add("Als");
EN_FIRST_LIST.add("Dry");
EN_FIRST_LIST.add("Bob");
EN_FIRST_LIST.add("Stowe");
EN_FIRST_LIST.add("Brid");
EN_FIRST_LIST.add("Chris");
EN_FIRST_LIST.add("Tru");
EN_FIRST_LIST.add("Thodore");
EN_FIRST_LIST.add("Tate");
EN_FIRST_LIST.add("Le");
EN_FIRST_LIST.add("Gwen");
EN_FIRST_LIST.add("Li");
EN_FIRST_LIST.add("Yule");
EN_FIRST_LIST.add("Bon");
EN_FIRST_LIST.add("Alick");
EN_FIRST_LIST.add("Saul");
EN_FIRST_LIST.add("Lo");
EN_FIRST_LIST.add("Rob");
EN_FIRST_LIST.add("Rod");
EN_FIRST_LIST.add("Bos");
EN_FIRST_LIST.add("Lu");
EN_FIRST_LIST.add("Deir");
EN_FIRST_LIST.add("Bow");
EN_FIRST_LIST.add("Ly");
EN_FIRST_LIST.add("Meg");
EN_FIRST_LIST.add("Vogt");
EN_FIRST_LIST.add("Ron");
EN_FIRST_LIST.add("Browning");
EN_FIRST_LIST.add("Nell");
EN_FIRST_LIST.add("Roo");
EN_FIRST_LIST.add("Ma");
EN_FIRST_LIST.add("Mel");
EN_FIRST_LIST.add("Broad");
EN_FIRST_LIST.add("Price");
EN_FIRST_LIST.add("Eve");
EN_FIRST_LIST.add("Jeames");
EN_FIRST_LIST.add("Mc");
EN_FIRST_LIST.add("Ros");
EN_FIRST_LIST.add("Me");
EN_FIRST_LIST.add("Mer");
EN_FIRST_LIST.add("Mi");
EN_FIRST_LIST.add("Wells");
EN_FIRST_LIST.add("Roy");
EN_FIRST_LIST.add("Kat");
EN_FIRST_LIST.add("Ann");
EN_FIRST_LIST.add("Drew");
EN_FIRST_LIST.add("Walk");
EN_FIRST_LIST.add("Giles");
EN_FIRST_LIST.add("Cro");
EN_FIRST_LIST.add("Mo");
EN_FIRST_LIST.add("Finn");
EN_FIRST_LIST.add("Quee");
EN_FIRST_LIST.add("Chur");
EN_FIRST_LIST.add("Kay");
EN_FIRST_LIST.add("Sher");
EN_FIRST_LIST.add("Berg");
EN_FIRST_LIST.add("Mu");
EN_FIRST_LIST.add("Cry");
EN_FIRST_LIST.add("Phoe");
EN_FIRST_LIST.add("Quen");
EN_FIRST_LIST.add("My");
EN_FIRST_LIST.add("Lamb");
EN_FIRST_LIST.add("Na");
EN_FIRST_LIST.add("Maltz");
EN_FIRST_LIST.add("Ne");
EN_FIRST_LIST.add("Dul");
EN_FIRST_LIST.add("Ni");
EN_FIRST_LIST.add("Glenn");
EN_FIRST_LIST.add("Dun");
EN_FIRST_LIST.add("Reade");
EN_FIRST_LIST.add("No");
EN_FIRST_LIST.add("Eips");
EN_FIRST_LIST.add("Lea");
EN_FIRST_LIST.add("Ny");
EN_FIRST_LIST.add("Duke");
EN_FIRST_LIST.add("Noah");
EN_FIRST_LIST.add("Lee");
EN_FIRST_LIST.add("Jac");
EN_FIRST_LIST.add("Bra");
EN_FIRST_LIST.add("Tur");
EN_FIRST_LIST.add("Faulk");
EN_FIRST_LIST.add("Lei");
EN_FIRST_LIST.add("Tut");
EN_FIRST_LIST.add("Len");
EN_FIRST_LIST.add("Oc");
EN_FIRST_LIST.add("Yvon");
EN_FIRST_LIST.add("Jan");
EN_FIRST_LIST.add("Leo");
EN_FIRST_LIST.add("Og");
EN_FIRST_LIST.add("Bert");
EN_FIRST_LIST.add("Les");
EN_FIRST_LIST.add("Shel");
EN_FIRST_LIST.add("Ol");
EN_FIRST_LIST.add("Shei");
EN_FIRST_LIST.add("Bro");
EN_FIRST_LIST.add("Lew");
EN_FIRST_LIST.add("Sta");
EN_FIRST_LIST.add("Jay");
EN_FIRST_LIST.add("Or");
EN_FIRST_LIST.add("Troll");
EN_FIRST_LIST.add("Os");
EN_FIRST_LIST.add("Bru");
EN_FIRST_LIST.add("Ralph");
EN_FIRST_LIST.add("Ste");
EN_FIRST_LIST.add("Ot");
EN_FIRST_LIST.add("Bald");
EN_FIRST_LIST.add("Blan");
EN_FIRST_LIST.add("Bry");
EN_FIRST_LIST.add("Pa");
EN_FIRST_LIST.add("Dunn");
EN_FIRST_LIST.add("Reed");
EN_FIRST_LIST.add("Pe");
EN_FIRST_LIST.add("Bush");
EN_FIRST_LIST.add("Theo");
EN_FIRST_LIST.add("Sweet");
EN_FIRST_LIST.add("Cooke");
EN_FIRST_LIST.add("Pi");
EN_FIRST_LIST.add("Cum");
EN_FIRST_LIST.add("Bess");
EN_FIRST_LIST.add("Po");
EN_FIRST_LIST.add("Cur");
EN_FIRST_LIST.add("Keith");
EN_FIRST_LIST.add("Cliff");
EN_FIRST_LIST.add("Gill");
EN_FIRST_LIST.add("Demp");
EN_FIRST_LIST.add("Pu");
EN_FIRST_LIST.add("Hous");
EN_FIRST_LIST.add("Poe");
EN_FIRST_LIST.add("Mid");
EN_FIRST_LIST.add("Mig");
EN_FIRST_LIST.add("Grote");
EN_FIRST_LIST.add("Spring");
EN_FIRST_LIST.add("Pol");
EN_FIRST_LIST.add("Abra");
EN_FIRST_LIST.add("Pop");
EN_FIRST_LIST.add("Mil");
EN_FIRST_LIST.add("Ara");
EN_FIRST_LIST.add("Sur");
EN_FIRST_LIST.add("Por");
EN_FIRST_LIST.add("Kel");
EN_FIRST_LIST.add("Min");
EN_FIRST_LIST.add("Ken");
EN_FIRST_LIST.add("Kep");
EN_FIRST_LIST.add("Bloom");
EN_FIRST_LIST.add("Ian");
EN_FIRST_LIST.add("Faithe");
EN_FIRST_LIST.add("Sean");
EN_FIRST_LIST.add("Fran");
EN_FIRST_LIST.add("Ker");
EN_FIRST_LIST.add("Bloor");
EN_FIRST_LIST.add("Sails");
EN_FIRST_LIST.add("Wheat");
EN_FIRST_LIST.add("Arm");
EN_FIRST_LIST.add("Key");
EN_FIRST_LIST.add("Quil");
EN_FIRST_LIST.add("Pull");
EN_FIRST_LIST.add("Hill");
EN_FIRST_LIST.add("Stan");
EN_FIRST_LIST.add("Kath");
EN_FIRST_LIST.add("Dodd");
EN_FIRST_LIST.add("Ra");
EN_FIRST_LIST.add("Quin");
EN_FIRST_LIST.add("Lionel");
EN_FIRST_LIST.add("Bron");
EN_FIRST_LIST.add("Jones");
EN_FIRST_LIST.add("Re");
EN_FIRST_LIST.add("Ri");
EN_FIRST_LIST.add("Bul");
EN_FIRST_LIST.add("Josh");
EN_FIRST_LIST.add("Clar");
EN_FIRST_LIST.add("Bun");
EN_FIRST_LIST.add("Wolf");
EN_FIRST_LIST.add("Ro");
EN_FIRST_LIST.add("Mans");
EN_FIRST_LIST.add("Tout");
EN_FIRST_LIST.add("Bur");
EN_FIRST_LIST.add("But");
EN_FIRST_LIST.add("Ru");
EN_FIRST_LIST.add("Ry");
EN_FIRST_LIST.add("Jef");
EN_FIRST_LIST.add("Noel");
EN_FIRST_LIST.add("Sa");
EN_FIRST_LIST.add("Lil");
EN_FIRST_LIST.add("Hag");
EN_FIRST_LIST.add("Lin");
EN_FIRST_LIST.add("Rus");
EN_FIRST_LIST.add("Se");
EN_FIRST_LIST.add("Hal");
EN_FIRST_LIST.add("Jen");
EN_FIRST_LIST.add("Han");
EN_FIRST_LIST.add("Ham");
EN_FIRST_LIST.add("Si");
EN_FIRST_LIST.add("Jer");
EN_FIRST_LIST.add("Har");
EN_FIRST_LIST.add("Shir");
EN_FIRST_LIST.add("Jes");
EN_FIRST_LIST.add("So");
EN_FIRST_LIST.add("Liz");
EN_FIRST_LIST.add("Scott");
EN_FIRST_LIST.add("Sains");
EN_FIRST_LIST.add("Haw");
EN_FIRST_LIST.add("Att");
EN_FIRST_LIST.add("Haz");
EN_FIRST_LIST.add("Hay");
EN_FIRST_LIST.add("Su");
EN_FIRST_LIST.add("Xan");
EN_FIRST_LIST.add("Sy");
EN_FIRST_LIST.add("Pri");
EN_FIRST_LIST.add("Yale");
EN_FIRST_LIST.add("Fitz");
EN_FIRST_LIST.add("Crom");
EN_FIRST_LIST.add("Strong");
EN_FIRST_LIST.add("Ta");
EN_FIRST_LIST.add("Harte");
EN_FIRST_LIST.add("Swin");
EN_FIRST_LIST.add("Leigh");
EN_FIRST_LIST.add("Yvette");
EN_FIRST_LIST.add("Te");
EN_FIRST_LIST.add("Pru");
EN_FIRST_LIST.add("Ti");
EN_FIRST_LIST.add("Ives");
EN_FIRST_LIST.add("Cyn");
EN_FIRST_LIST.add("To");
EN_FIRST_LIST.add("Aus");
EN_FIRST_LIST.add("Gray");
EN_FIRST_LIST.add("Ty");
EN_FIRST_LIST.add("Syl");
EN_FIRST_LIST.add("Wylde");
EN_FIRST_LIST.add("Fred");
EN_FIRST_LIST.add("Yonng");
EN_FIRST_LIST.add("Free");
EN_FIRST_LIST.add("Kim");
EN_FIRST_LIST.add("Nor");
EN_FIRST_LIST.add("Miles");
EN_FIRST_LIST.add("Penn");
EN_FIRST_LIST.add("Gal");
EN_FIRST_LIST.add("Kip");
EN_FIRST_LIST.add("Yea");
EN_FIRST_LIST.add("Ward");
EN_FIRST_LIST.add("Vaug");
EN_FIRST_LIST.add("Keats");
EN_FIRST_LIST.add("Kit");
EN_FIRST_LIST.add("Long");
EN_FIRST_LIST.add("Gas");
EN_FIRST_LIST.add("Gar");
EN_FIRST_LIST.add("Yed");
EN_FIRST_LIST.add("Up");
EN_FIRST_LIST.add("Wag");
EN_FIRST_LIST.add("Holmes");
EN_FIRST_LIST.add("Ur");
EN_FIRST_LIST.add("Camp");
EN_FIRST_LIST.add("Simp");
EN_FIRST_LIST.add("Brown");
EN_FIRST_LIST.add("Wal");
EN_FIRST_LIST.add("Watt");
EN_FIRST_LIST.add("Wan");
EN_FIRST_LIST.add("Yer");
EN_FIRST_LIST.add("Wright");
EN_FIRST_LIST.add("Yet");
EN_FIRST_LIST.add("Mark");
EN_FIRST_LIST.add("Clare");
EN_FIRST_LIST.add("War");
EN_FIRST_LIST.add("Va");
EN_FIRST_LIST.add("Wat");
EN_FIRST_LIST.add("Greg");
EN_FIRST_LIST.add("Funk");
EN_FIRST_LIST.add("Bard");
EN_FIRST_LIST.add("Way");
EN_FIRST_LIST.add("Stel");
EN_FIRST_LIST.add("Camil");
EN_FIRST_LIST.add("Ve");
EN_FIRST_LIST.add("Dutt");
EN_FIRST_LIST.add("Clark");
EN_FIRST_LIST.add("Vi");
EN_FIRST_LIST.add("Toyn");
EN_FIRST_LIST.add("Mond");
EN_FIRST_LIST.add("Grey");
EN_FIRST_LIST.add("Wood");
EN_FIRST_LIST.add("Moi");
EN_FIRST_LIST.add("Hed");
EN_FIRST_LIST.add("Pul");
EN_FIRST_LIST.add("Moll");
EN_FIRST_LIST.add("Wa");
EN_FIRST_LIST.add("Jean");
EN_FIRST_LIST.add("Mol");
EN_FIRST_LIST.add("Moo");
EN_FIRST_LIST.add("Hugh");
EN_FIRST_LIST.add("Mon");
EN_FIRST_LIST.add("Stein");
EN_FIRST_LIST.add("Jim");
EN_FIRST_LIST.add("Hen");
EN_FIRST_LIST.add("Bruce");
EN_FIRST_LIST.add("Mor");
EN_FIRST_LIST.add("Wh");
EN_FIRST_LIST.add("Fan");
EN_FIRST_LIST.add("Wi");
EN_FIRST_LIST.add("Mot");
EN_FIRST_LIST.add("Her");
EN_FIRST_LIST.add("Pound");
EN_FIRST_LIST.add("Wo");
EN_FIRST_LIST.add("Hew");
EN_FIRST_LIST.add("Wool");
EN_FIRST_LIST.add("Green");
EN_FIRST_LIST.add("Bart");
EN_FIRST_LIST.add("Fay");
EN_FIRST_LIST.add("Zim");
EN_FIRST_LIST.add("Mick");
EN_FIRST_LIST.add("Wy");
EN_FIRST_LIST.add("Van");
EN_FIRST_LIST.add("Word");
EN_FIRST_LIST.add("Thorn");
EN_FIRST_LIST.add("Sharp");
EN_FIRST_LIST.add("Judd");
EN_FIRST_LIST.add("Xa");
EN_FIRST_LIST.add("Xe");
EN_FIRST_LIST.add("Phyl");
EN_FIRST_LIST.add("Matt");
EN_FIRST_LIST.add("Twain");
EN_FIRST_LIST.add("Gene");
EN_FIRST_LIST.add("Dwight");
EN_FIRST_LIST.add("Child");
EN_FIRST_LIST.add("Carr");
EN_FIRST_LIST.add("Carl");
EN_FIRST_LIST.add("Smith");
EN_FIRST_LIST.add("House");
EN_FIRST_LIST.add("Lon");
EN_FIRST_LIST.add("Ye");
EN_FIRST_LIST.add("Mont");
EN_FIRST_LIST.add("Gem");
EN_FIRST_LIST.add("Lor");
EN_FIRST_LIST.add("Lou");
EN_FIRST_LIST.add("Ear");
EN_FIRST_LIST.add("Jill");
EN_FIRST_LIST.add("Geor");
EN_FIRST_LIST.add("Wen");
EN_FIRST_LIST.add("Stil");
EN_FIRST_LIST.add("Wes");
EN_FIRST_LIST.add("Wer");
EN_FIRST_LIST.add("Za");
EN_FIRST_LIST.add("Cook");
EN_FIRST_LIST.add("Chad");
EN_FIRST_LIST.add("Cleve");
EN_FIRST_LIST.add("Grif");
EN_FIRST_LIST.add("Ze");
EN_FIRST_LIST.add("Cash");
EN_FIRST_LIST.add("Cham");
EN_FIRST_LIST.add("Joyce");
EN_FIRST_LIST.add("More");
EN_FIRST_LIST.add("Chan");
EN_FIRST_LIST.add("Loui");
EN_FIRST_LIST.add("Chap");
EN_FIRST_LIST.add("Thom");
EN_FIRST_LIST.add("Zo");
EN_FIRST_LIST.add("Char");
EN_FIRST_LIST.add("Chau");
EN_FIRST_LIST.add("Maug");
EN_FIRST_LIST.add("Priest");
EN_FIRST_LIST.add("Maud");
EN_FIRST_LIST.add("Zang");
EN_FIRST_LIST.add("Crofts");
EN_FIRST_LIST.add("Hil");
EN_FIRST_LIST.add("Fel");
EN_FIRST_LIST.add("Dai");
EN_FIRST_LIST.add("Dal");
EN_FIRST_LIST.add("Dan");
EN_FIRST_LIST.add("Cons");
EN_FIRST_LIST.add("Veb");
EN_FIRST_LIST.add("Fer");
EN_FIRST_LIST.add("Dar");
EN_FIRST_LIST.add("Geof");
EN_FIRST_LIST.add("Blair");
EN_FIRST_LIST.add("Tab");
EN_FIRST_LIST.add("Jeff");
EN_FIRST_LIST.add("Whee");
EN_FIRST_LIST.add("Wilhel");
EN_FIRST_LIST.add("Chloe");
EN_FIRST_LIST.add("Borg");
EN_FIRST_LIST.add("Tam");
EN_FIRST_LIST.add("Ver");
EN_FIRST_LIST.add("Grace");
EN_FIRST_LIST.add("Webb");
EN_FIRST_LIST.add("Quinn");
EN_FIRST_LIST.add("Tay");
EN_FIRST_LIST.add("Burne");
EN_FIRST_LIST.add("King");
EN_FIRST_LIST.add("Webs");
EN_FIRST_LIST.add("Job");
EN_FIRST_LIST.add("Roxan");
EN_FIRST_LIST.add("Joe");
EN_FIRST_LIST.add("Gib");
EN_FIRST_LIST.add("Kyle");
EN_FIRST_LIST.add("Cae");
EN_FIRST_LIST.add("Nick");
EN_FIRST_LIST.add("Hume");
EN_FIRST_LIST.add("Jon");
EN_FIRST_LIST.add("Mur");
EN_FIRST_LIST.add("Gil");
EN_FIRST_LIST.add("Jor");
EN_FIRST_LIST.add("Louie");
EN_FIRST_LIST.add("Cal");
EN_FIRST_LIST.add("Gis");
EN_FIRST_LIST.add("Jou");
EN_FIRST_LIST.add("Can");
EN_FIRST_LIST.add("Zoe");
EN_FIRST_LIST.add("Car");
EN_FIRST_LIST.add("Joy");
EN_FIRST_LIST.add("Wil");
EN_FIRST_LIST.add("Burns");
EN_FIRST_LIST.add("Gail");
EN_FIRST_LIST.add("Win");
EN_FIRST_LIST.add("Sam");
EN_FIRST_LIST.add("Sal");
EN_FIRST_LIST.add("Louis");
EN_FIRST_LIST.add("Spen");
EN_FIRST_LIST.add("San");
EN_FIRST_LIST.add("Wild");
EN_FIRST_LIST.add("Sas");
EN_FIRST_LIST.add("York");
EN_FIRST_LIST.add("Lance");
EN_FIRST_LIST.add("Beau");
EN_FIRST_LIST.add("Saw");
EN_FIRST_LIST.add("Hodg");
EN_FIRST_LIST.add("Glad");
EN_FIRST_LIST.add("Claude");
EN_FIRST_LIST.add("Sax");
EN_FIRST_LIST.add("Brook");
EN_FIRST_LIST.add("Kings");
EN_FIRST_LIST.add("Cher");
EN_FIRST_LIST.add("Gale");
EN_FIRST_LIST.add("Ches");
EN_FIRST_LIST.add("Rhys");
EN_FIRST_LIST.add("Earl");
EN_FIRST_LIST.add("Will");
EN_FIRST_LIST.add("Pritt");
EN_FIRST_LIST.add("Rusk");
EN_FIRST_LIST.add("Jack");
EN_FIRST_LIST.add("Deb");
EN_FIRST_LIST.add("Bab");
EN_FIRST_LIST.add("Flower");
EN_FIRST_LIST.add("Fin");
EN_FIRST_LIST.add("O'Neil");
EN_FIRST_LIST.add("Den");
EN_FIRST_LIST.add("Dick");
EN_FIRST_LIST.add("Thomp");
EN_FIRST_LIST.add("Der");
EN_FIRST_LIST.add("Vic");
EN_FIRST_LIST.add("Bar");
EN_FIRST_LIST.add("Ted");
EN_FIRST_LIST.add("Boyle");
EN_FIRST_LIST.add("Stuart");
EN_FIRST_LIST.add("Whit");
EN_FIRST_LIST.add("Bau");
EN_FIRST_LIST.add("Rae");
EN_FIRST_LIST.add("Blume");
EN_FIRST_LIST.add("Vin");
EN_FIRST_LIST.add("Bryce");
EN_FIRST_LIST.add("Ten");
EN_FIRST_LIST.add("Gla");
EN_FIRST_LIST.add("Vio");
EN_FIRST_LIST.add("Moul");
EN_FIRST_LIST.add("Tem");
EN_FIRST_LIST.add("Vir");
EN_FIRST_LIST.add("Ran");
}
public static void initEN_LAST_LIST() {
EN_LAST_LIST.add("nings");
EN_LAST_LIST.add("hale");
EN_LAST_LIST.add("lvis");
EN_LAST_LIST.add("hall");
EN_LAST_LIST.add("todd");
EN_LAST_LIST.add("via");
EN_LAST_LIST.add("vid");
EN_LAST_LIST.add("liot");
EN_LAST_LIST.add("vic");
EN_LAST_LIST.add("ted");
EN_LAST_LIST.add("rad");
EN_LAST_LIST.add("rae");
EN_LAST_LIST.add("rah");
EN_LAST_LIST.add("vin");
EN_LAST_LIST.add("ral");
EN_LAST_LIST.add("ten");
EN_LAST_LIST.add("ram");
EN_LAST_LIST.add("ter");
EN_LAST_LIST.add("vis");
EN_LAST_LIST.add("tes");
EN_LAST_LIST.add("thus");
EN_LAST_LIST.add("thur");
EN_LAST_LIST.add("ray");
EN_LAST_LIST.add("lins");
EN_LAST_LIST.add("pont");
EN_LAST_LIST.add("dawn");
EN_LAST_LIST.add("glenn");
EN_LAST_LIST.add("kuk");
EN_LAST_LIST.add("rold");
EN_LAST_LIST.add("cliff");
EN_LAST_LIST.add("roll");
EN_LAST_LIST.add("gold");
EN_LAST_LIST.add("cer");
EN_LAST_LIST.add("xon");
EN_LAST_LIST.add("cey");
EN_LAST_LIST.add("browne");
EN_LAST_LIST.add("scott");
EN_LAST_LIST.add("a");
EN_LAST_LIST.add("rwood");
EN_LAST_LIST.add("leif");
EN_LAST_LIST.add("h");
EN_LAST_LIST.add("tha");
EN_LAST_LIST.add("n");
EN_LAST_LIST.add("o");
EN_LAST_LIST.add("the");
EN_LAST_LIST.add("fast");
EN_LAST_LIST.add("frances");
EN_LAST_LIST.add("y");
EN_LAST_LIST.add("clife");
EN_LAST_LIST.add("sweet");
EN_LAST_LIST.add("muel");
EN_LAST_LIST.add("rone");
EN_LAST_LIST.add("lith");
EN_LAST_LIST.add("thy");
EN_LAST_LIST.add("ning");
EN_LAST_LIST.add("chill");
EN_LAST_LIST.add("gou");
EN_LAST_LIST.add("tia");
EN_LAST_LIST.add("litt");
EN_LAST_LIST.add("red");
EN_LAST_LIST.add("thorne");
EN_LAST_LIST.add("tie");
EN_LAST_LIST.add("rian");
EN_LAST_LIST.add("reg");
EN_LAST_LIST.add("riam");
EN_LAST_LIST.add("pag");
EN_LAST_LIST.add("tin");
EN_LAST_LIST.add("rel");
EN_LAST_LIST.add("tim");
EN_LAST_LIST.add("ren");
EN_LAST_LIST.add("tio");
EN_LAST_LIST.add("rias");
EN_LAST_LIST.add("swift");
EN_LAST_LIST.add("tis");
EN_LAST_LIST.add("ret");
EN_LAST_LIST.add("che");
EN_LAST_LIST.add("res");
EN_LAST_LIST.add("rex");
EN_LAST_LIST.add("chi");
EN_LAST_LIST.add("lace");
EN_LAST_LIST.add("rey");
EN_LAST_LIST.add("riah");
EN_LAST_LIST.add("holmes");
EN_LAST_LIST.add("phine");
EN_LAST_LIST.add("yves");
EN_LAST_LIST.add("cia");
EN_LAST_LIST.add("cie");
EN_LAST_LIST.add("child");
EN_LAST_LIST.add("young");
EN_LAST_LIST.add("cil");
EN_LAST_LIST.add("hart");
EN_LAST_LIST.add("cis");
EN_LAST_LIST.add("miles");
EN_LAST_LIST.add("ridge");
EN_LAST_LIST.add("bruce");
EN_LAST_LIST.add("live");
EN_LAST_LIST.add("lius");
EN_LAST_LIST.add("rick");
EN_LAST_LIST.add("tle");
EN_LAST_LIST.add("nior");
EN_LAST_LIST.add("crofts");
EN_LAST_LIST.add("well");
EN_LAST_LIST.add("cke");
EN_LAST_LIST.add("sworth");
EN_LAST_LIST.add("ria");
EN_LAST_LIST.add("rid");
EN_LAST_LIST.add("ric");
EN_LAST_LIST.add("wylde");
EN_LAST_LIST.add("rie");
EN_LAST_LIST.add("cky");
EN_LAST_LIST.add("ries");
EN_LAST_LIST.add("peg");
EN_LAST_LIST.add("riet");
EN_LAST_LIST.add("nah");
EN_LAST_LIST.add("ril");
EN_LAST_LIST.add("keats");
EN_LAST_LIST.add("pel");
EN_LAST_LIST.add("rin");
EN_LAST_LIST.add("nal");
EN_LAST_LIST.add("nan");
EN_LAST_LIST.add("per");
EN_LAST_LIST.add("ris");
EN_LAST_LIST.add("jane");
EN_LAST_LIST.add("nat");
EN_LAST_LIST.add("nas");
EN_LAST_LIST.add("raine");
EN_LAST_LIST.add("neil");
EN_LAST_LIST.add("quinn");
EN_LAST_LIST.add("riel");
EN_LAST_LIST.add("faithe");
EN_LAST_LIST.add("gue");
EN_LAST_LIST.add("braith");
EN_LAST_LIST.add("gus");
EN_LAST_LIST.add("nell");
EN_LAST_LIST.add("guy");
EN_LAST_LIST.add("saul");
EN_LAST_LIST.add("vogt");
EN_LAST_LIST.add("ton");
EN_LAST_LIST.add("tom");
EN_LAST_LIST.add("tance");
EN_LAST_LIST.add("tian");
EN_LAST_LIST.add("tor");
EN_LAST_LIST.add("lain");
EN_LAST_LIST.add("mund");
EN_LAST_LIST.add("sharp");
EN_LAST_LIST.add("sham");
EN_LAST_LIST.add("cob");
EN_LAST_LIST.add("twain");
EN_LAST_LIST.add("shaw");
EN_LAST_LIST.add("nise");
EN_LAST_LIST.add("phy");
EN_LAST_LIST.add("col");
EN_LAST_LIST.add("con");
EN_LAST_LIST.add("duke");
EN_LAST_LIST.add("cent");
EN_LAST_LIST.add("phael");
EN_LAST_LIST.add("lett");
EN_LAST_LIST.add("cox");
EN_LAST_LIST.add("nee");
EN_LAST_LIST.add("reau");
EN_LAST_LIST.add("nel");
EN_LAST_LIST.add("lan");
EN_LAST_LIST.add("pir");
EN_LAST_LIST.add("ner");
EN_LAST_LIST.add("lap");
EN_LAST_LIST.add("ale");
EN_LAST_LIST.add("net");
EN_LAST_LIST.add("nes");
EN_LAST_LIST.add("las");
EN_LAST_LIST.add("tra");
EN_LAST_LIST.add("law");
EN_LAST_LIST.add("ney");
EN_LAST_LIST.add("lay");
EN_LAST_LIST.add("shall");
EN_LAST_LIST.add("phens");
EN_LAST_LIST.add("cius");
EN_LAST_LIST.add("snow");
EN_LAST_LIST.add("rob");
EN_LAST_LIST.add("rod");
EN_LAST_LIST.add("bush");
EN_LAST_LIST.add("roe");
EN_LAST_LIST.add("trick");
EN_LAST_LIST.add("rol");
EN_LAST_LIST.add("ron");
EN_LAST_LIST.add("bryce");
EN_LAST_LIST.add("gill");
EN_LAST_LIST.add("tier");
EN_LAST_LIST.add("blume");
EN_LAST_LIST.add("trice");
EN_LAST_LIST.add("land");
EN_LAST_LIST.add("roy");
EN_LAST_LIST.add("ann");
EN_LAST_LIST.add("tta");
EN_LAST_LIST.add("ple");
EN_LAST_LIST.add("phrey");
EN_LAST_LIST.add("wald");
EN_LAST_LIST.add("lamb");
EN_LAST_LIST.add("nence");
EN_LAST_LIST.add("nia");
EN_LAST_LIST.add("nid");
EN_LAST_LIST.add("nic");
EN_LAST_LIST.add("nie");
EN_LAST_LIST.add("lee");
EN_LAST_LIST.add("jah");
EN_LAST_LIST.add("nin");
EN_LAST_LIST.add("tus");
EN_LAST_LIST.add("len");
EN_LAST_LIST.add("nio");
EN_LAST_LIST.add("vian");
EN_LAST_LIST.add("gins");
EN_LAST_LIST.add("elroy");
EN_LAST_LIST.add("ler");
EN_LAST_LIST.add("nis");
EN_LAST_LIST.add("bois");
EN_LAST_LIST.add("let");
EN_LAST_LIST.add("les");
EN_LAST_LIST.add("rine");
EN_LAST_LIST.add("nix");
EN_LAST_LIST.add("lew");
EN_LAST_LIST.add("ley");
EN_LAST_LIST.add("jay");
EN_LAST_LIST.add("tosh");
EN_LAST_LIST.add("reed");
EN_LAST_LIST.add("reen");
EN_LAST_LIST.add("baird");
EN_LAST_LIST.add("bohm");
EN_LAST_LIST.add("dunn");
EN_LAST_LIST.add("brooke");
EN_LAST_LIST.add("cus");
EN_LAST_LIST.add("penn");
EN_LAST_LIST.add("nett");
EN_LAST_LIST.add("poe");
EN_LAST_LIST.add("ward");
EN_LAST_LIST.add("worth");
EN_LAST_LIST.add("pkins");
EN_LAST_LIST.add("gray");
EN_LAST_LIST.add("lard");
EN_LAST_LIST.add("grace");
EN_LAST_LIST.add("nald");
EN_LAST_LIST.add("vice");
EN_LAST_LIST.add("rion");
EN_LAST_LIST.add("dodd");
EN_LAST_LIST.add("peare");
EN_LAST_LIST.add("gram");
EN_LAST_LIST.add("yan");
EN_LAST_LIST.add("black");
EN_LAST_LIST.add("nest");
EN_LAST_LIST.add("tout");
EN_LAST_LIST.add("chard");
EN_LAST_LIST.add("smith");
EN_LAST_LIST.add("lia");
EN_LAST_LIST.add("lie");
EN_LAST_LIST.add("lynch");
EN_LAST_LIST.add("lin");
EN_LAST_LIST.add("pril");
EN_LAST_LIST.add("moll");
EN_LAST_LIST.add("hal");
EN_LAST_LIST.add("lip");
EN_LAST_LIST.add("han");
EN_LAST_LIST.add("ham");
EN_LAST_LIST.add("piers");
EN_LAST_LIST.add("lis");
EN_LAST_LIST.add("bias");
EN_LAST_LIST.add("vier");
EN_LAST_LIST.add("bian");
EN_LAST_LIST.add("lix");
EN_LAST_LIST.add("nand");
EN_LAST_LIST.add("liz");
EN_LAST_LIST.add("hugh");
EN_LAST_LIST.add("lass");
EN_LAST_LIST.add("ives");
EN_LAST_LIST.add("vien");
EN_LAST_LIST.add("camp");
EN_LAST_LIST.add("kiel");
EN_LAST_LIST.add("boyce");
EN_LAST_LIST.add("yale");
EN_LAST_LIST.add("shop");
EN_LAST_LIST.add("pert");
EN_LAST_LIST.add("rell");
EN_LAST_LIST.add("non");
EN_LAST_LIST.add("house");
EN_LAST_LIST.add("nor");
EN_LAST_LIST.add("mons");
EN_LAST_LIST.add("tine");
EN_LAST_LIST.add("rite");
EN_LAST_LIST.add("green");
EN_LAST_LIST.add("race");
EN_LAST_LIST.add("yes");
EN_LAST_LIST.add("yer");
EN_LAST_LIST.add("war");
EN_LAST_LIST.add("yet");
EN_LAST_LIST.add("wat");
EN_LAST_LIST.add("mond");
EN_LAST_LIST.add("way");
EN_LAST_LIST.add("grey");
EN_LAST_LIST.add("miah");
EN_LAST_LIST.add("drich");
EN_LAST_LIST.add("funk");
EN_LAST_LIST.add("watt");
EN_LAST_LIST.add("greg");
EN_LAST_LIST.add("dutt");
EN_LAST_LIST.add("ryl");
EN_LAST_LIST.add("croft");
EN_LAST_LIST.add("jim");
EN_LAST_LIST.add("alick");
EN_LAST_LIST.add("nard");
EN_LAST_LIST.add("broad");
EN_LAST_LIST.add("fax");
EN_LAST_LIST.add("tram");
EN_LAST_LIST.add("cash");
EN_LAST_LIST.add("rene");
EN_LAST_LIST.add("fay");
EN_LAST_LIST.add("tion");
EN_LAST_LIST.add("gene");
EN_LAST_LIST.add("harte");
EN_LAST_LIST.add("carr");
EN_LAST_LIST.add("niell");
EN_LAST_LIST.add("mick");
EN_LAST_LIST.add("judd");
EN_LAST_LIST.add("loc");
EN_LAST_LIST.add("diah");
EN_LAST_LIST.add("bright");
EN_LAST_LIST.add("lon");
EN_LAST_LIST.add("dolph");
EN_LAST_LIST.add("lop");
EN_LAST_LIST.add("gail");
EN_LAST_LIST.add("lor");
EN_LAST_LIST.add("lot");
EN_LAST_LIST.add("lou");
EN_LAST_LIST.add("hume");
EN_LAST_LIST.add("low");
EN_LAST_LIST.add("tein");
EN_LAST_LIST.add("wen");
EN_LAST_LIST.add("wer");
EN_LAST_LIST.add("more");
EN_LAST_LIST.add("chad");
EN_LAST_LIST.add("born");
EN_LAST_LIST.add("dolf");
EN_LAST_LIST.add("wey");
EN_LAST_LIST.add("borg");
EN_LAST_LIST.add("grid");
EN_LAST_LIST.add("dick");
EN_LAST_LIST.add("chell");
EN_LAST_LIST.add("dad");
EN_LAST_LIST.add("dice");
EN_LAST_LIST.add("pys");
EN_LAST_LIST.add("whit");
EN_LAST_LIST.add("nus");
EN_LAST_LIST.add("gess");
EN_LAST_LIST.add("dan");
EN_LAST_LIST.add("dam");
EN_LAST_LIST.add("mott");
EN_LAST_LIST.add("kins");
EN_LAST_LIST.add("fer");
EN_LAST_LIST.add("shua");
EN_LAST_LIST.add("beau");
EN_LAST_LIST.add("dict");
EN_LAST_LIST.add("ving");
EN_LAST_LIST.add("fey");
EN_LAST_LIST.add("day");
EN_LAST_LIST.add("bloor");
EN_LAST_LIST.add("bott");
EN_LAST_LIST.add("king");
EN_LAST_LIST.add("grote");
EN_LAST_LIST.add("job");
EN_LAST_LIST.add("joe");
EN_LAST_LIST.add("beck");
EN_LAST_LIST.add("mike");
EN_LAST_LIST.add("rett");
EN_LAST_LIST.add("dore");
EN_LAST_LIST.add("rald");
EN_LAST_LIST.add("joy");
EN_LAST_LIST.add("win");
EN_LAST_LIST.add("sam");
EN_LAST_LIST.add("wis");
EN_LAST_LIST.add("chael");
EN_LAST_LIST.add("san");
EN_LAST_LIST.add("glan");
EN_LAST_LIST.add("chel");
EN_LAST_LIST.add("gale");
EN_LAST_LIST.add("sar");
EN_LAST_LIST.add("glas");
EN_LAST_LIST.add("say");
EN_LAST_LIST.add("maltz");
EN_LAST_LIST.add("lyle");
EN_LAST_LIST.add("chey");
EN_LAST_LIST.add("earl");
EN_LAST_LIST.add("cher");
EN_LAST_LIST.add("fie");
EN_LAST_LIST.add("joan");
EN_LAST_LIST.add("lup");
EN_LAST_LIST.add("del");
EN_LAST_LIST.add("lus");
EN_LAST_LIST.add("den");
EN_LAST_LIST.add("der");
EN_LAST_LIST.add("pham");
EN_LAST_LIST.add("bar");
EN_LAST_LIST.add("des");
EN_LAST_LIST.add("ac");
EN_LAST_LIST.add("giles");
EN_LAST_LIST.add("kirk");
EN_LAST_LIST.add("ah");
EN_LAST_LIST.add("bill");
EN_LAST_LIST.add("leste");
EN_LAST_LIST.add("an");
EN_LAST_LIST.add("trid");
EN_LAST_LIST.add("mill");
EN_LAST_LIST.add("boyd");
EN_LAST_LIST.add("bby");
EN_LAST_LIST.add("jones");
EN_LAST_LIST.add("lynn");
EN_LAST_LIST.add("frank");
EN_LAST_LIST.add("velt");
EN_LAST_LIST.add("dean");
EN_LAST_LIST.add("strong");
EN_LAST_LIST.add("dge");
EN_LAST_LIST.add("be");
EN_LAST_LIST.add("ters");
EN_LAST_LIST.add("rence");
EN_LAST_LIST.add("sea");
EN_LAST_LIST.add("xine");
EN_LAST_LIST.add("laine");
EN_LAST_LIST.add("by");
EN_LAST_LIST.add("sel");
EN_LAST_LIST.add("sen");
EN_LAST_LIST.add("ca");
EN_LAST_LIST.add("ses");
EN_LAST_LIST.add("ser");
EN_LAST_LIST.add("ce");
EN_LAST_LIST.add("bins");
EN_LAST_LIST.add("ch");
EN_LAST_LIST.add("sey");
EN_LAST_LIST.add("ck");
EN_LAST_LIST.add("kell");
EN_LAST_LIST.add("co");
EN_LAST_LIST.add("bing");
EN_LAST_LIST.add("june");
EN_LAST_LIST.add("cy");
EN_LAST_LIST.add("paul");
EN_LAST_LIST.add("hutt");
EN_LAST_LIST.add("da");
EN_LAST_LIST.add("dia");
EN_LAST_LIST.add("lyn");
EN_LAST_LIST.add("die");
EN_LAST_LIST.add("de");
EN_LAST_LIST.add("bee");
EN_LAST_LIST.add("di");
EN_LAST_LIST.add("bel");
EN_LAST_LIST.add("dn");
EN_LAST_LIST.add("ben");
EN_LAST_LIST.add("ford");
EN_LAST_LIST.add("do");
EN_LAST_LIST.add("pher");
EN_LAST_LIST.add("bes");
EN_LAST_LIST.add("claude");
EN_LAST_LIST.add("kent");
EN_LAST_LIST.add("dy");
EN_LAST_LIST.add("phen");
EN_LAST_LIST.add("bey");
EN_LAST_LIST.add("bird");
EN_LAST_LIST.add("joel");
EN_LAST_LIST.add("nuel");
EN_LAST_LIST.add("ed");
EN_LAST_LIST.add("ralph");
EN_LAST_LIST.add("el");
EN_LAST_LIST.add("tess");
EN_LAST_LIST.add("brown");
EN_LAST_LIST.add("er");
EN_LAST_LIST.add("dike");
EN_LAST_LIST.add("chards");
EN_LAST_LIST.add("foe");
EN_LAST_LIST.add("fe");
EN_LAST_LIST.add("back");
EN_LAST_LIST.add("bach");
EN_LAST_LIST.add("sia");
EN_LAST_LIST.add("sie");
EN_LAST_LIST.add("fox");
EN_LAST_LIST.add("sid");
EN_LAST_LIST.add("leigh");
EN_LAST_LIST.add("pound");
EN_LAST_LIST.add("dine");
EN_LAST_LIST.add("fy");
EN_LAST_LIST.add("leign");
EN_LAST_LIST.add("sil");
EN_LAST_LIST.add("ga");
EN_LAST_LIST.add("ge");
EN_LAST_LIST.add("troy");
EN_LAST_LIST.add("dwight");
EN_LAST_LIST.add("nions");
EN_LAST_LIST.add("go");
EN_LAST_LIST.add("soll");
EN_LAST_LIST.add("greve");
EN_LAST_LIST.add("clare");
EN_LAST_LIST.add("vieve");
EN_LAST_LIST.add("gy");
EN_LAST_LIST.add("clark");
EN_LAST_LIST.add("hue");
EN_LAST_LIST.add("fort");
EN_LAST_LIST.add("bia");
EN_LAST_LIST.add("grant");
EN_LAST_LIST.add("he");
EN_LAST_LIST.add("holt");
EN_LAST_LIST.add("hum");
EN_LAST_LIST.add("bin");
EN_LAST_LIST.add("yonng");
EN_LAST_LIST.add("soon");
EN_LAST_LIST.add("hy");
EN_LAST_LIST.add("fra");
EN_LAST_LIST.add("chloe");
EN_LAST_LIST.add("briel");
EN_LAST_LIST.add("burns");
EN_LAST_LIST.add("phia");
EN_LAST_LIST.add("kerr");
EN_LAST_LIST.add("bitt");
EN_LAST_LIST.add("tience");
EN_LAST_LIST.add("brey");
EN_LAST_LIST.add("hood");
EN_LAST_LIST.add("bell");
EN_LAST_LIST.add("phil");
EN_LAST_LIST.add("field");
EN_LAST_LIST.add("steele");
EN_LAST_LIST.add("pritt");
EN_LAST_LIST.add("john");
EN_LAST_LIST.add("je");
EN_LAST_LIST.add("joyce");
EN_LAST_LIST.add("don");
EN_LAST_LIST.add("jo");
EN_LAST_LIST.add("jy");
EN_LAST_LIST.add("mag");
EN_LAST_LIST.add("blair");
EN_LAST_LIST.add("ke");
EN_LAST_LIST.add("man");
EN_LAST_LIST.add("mas");
EN_LAST_LIST.add("mar");
EN_LAST_LIST.add("may");
EN_LAST_LIST.add("max");
EN_LAST_LIST.add("sopp");
EN_LAST_LIST.add("ment");
EN_LAST_LIST.add("mens");
EN_LAST_LIST.add("ky");
EN_LAST_LIST.add("o'neil");
EN_LAST_LIST.add("la");
EN_LAST_LIST.add("le");
EN_LAST_LIST.add("stuart");
EN_LAST_LIST.add("li");
EN_LAST_LIST.add("ghes");
EN_LAST_LIST.add("hicks");
EN_LAST_LIST.add("dred");
EN_LAST_LIST.add("lo");
EN_LAST_LIST.add("drea");
EN_LAST_LIST.add("vans");
EN_LAST_LIST.add("ly");
EN_LAST_LIST.add("wright");
EN_LAST_LIST.add("som");
EN_LAST_LIST.add("logg");
EN_LAST_LIST.add("dra");
EN_LAST_LIST.add("son");
EN_LAST_LIST.add("ma");
EN_LAST_LIST.add("tham");
EN_LAST_LIST.add("berg");
EN_LAST_LIST.add("dith");
EN_LAST_LIST.add("dre");
EN_LAST_LIST.add("than");
EN_LAST_LIST.add("sor");
EN_LAST_LIST.add("me");
EN_LAST_LIST.add("noah");
EN_LAST_LIST.add("phne");
EN_LAST_LIST.add("brian");
EN_LAST_LIST.add("brook");
EN_LAST_LIST.add("mo");
EN_LAST_LIST.add("harine");
EN_LAST_LIST.add("lance");
EN_LAST_LIST.add("tate");
EN_LAST_LIST.add("my");
EN_LAST_LIST.add("yule");
EN_LAST_LIST.add("na");
EN_LAST_LIST.add("bob");
EN_LAST_LIST.add("nd");
EN_LAST_LIST.add("ne");
EN_LAST_LIST.add("bon");
EN_LAST_LIST.add("no");
EN_LAST_LIST.add("louie");
EN_LAST_LIST.add("sean");
EN_LAST_LIST.add("ny");
EN_LAST_LIST.add("bess");
EN_LAST_LIST.add("meg");
EN_LAST_LIST.add("tiane");
EN_LAST_LIST.add("head");
EN_LAST_LIST.add("hous");
EN_LAST_LIST.add("meo");
EN_LAST_LIST.add("men");
EN_LAST_LIST.add("beth");
EN_LAST_LIST.add("bald");
EN_LAST_LIST.add("louis");
EN_LAST_LIST.add("mer");
EN_LAST_LIST.add("boyle");
EN_LAST_LIST.add("mew");
EN_LAST_LIST.add("ville");
EN_LAST_LIST.add("kay");
EN_LAST_LIST.add("clair");
EN_LAST_LIST.add("tave");
EN_LAST_LIST.add("bert");
EN_LAST_LIST.add("finn");
EN_LAST_LIST.add("drey");
EN_LAST_LIST.add("burne");
EN_LAST_LIST.add("drew");
EN_LAST_LIST.add("dell");
EN_LAST_LIST.add("pe");
EN_LAST_LIST.add("fitch");
EN_LAST_LIST.add("ps");
EN_LAST_LIST.add("dric");
EN_LAST_LIST.add("beard");
EN_LAST_LIST.add("py");
EN_LAST_LIST.add("walsh");
EN_LAST_LIST.add("thew");
EN_LAST_LIST.add("qe");
EN_LAST_LIST.add("chols");
EN_LAST_LIST.add("brow");
EN_LAST_LIST.add("ther");
EN_LAST_LIST.add("noel");
EN_LAST_LIST.add("they");
EN_LAST_LIST.add("clough");
EN_LAST_LIST.add("thea");
EN_LAST_LIST.add("ckens");
EN_LAST_LIST.add("qy");
EN_LAST_LIST.add("thel");
EN_LAST_LIST.add("ra");
EN_LAST_LIST.add("booth");
EN_LAST_LIST.add("re");
EN_LAST_LIST.add("trine");
EN_LAST_LIST.add("rl");
EN_LAST_LIST.add("loise");
EN_LAST_LIST.add("ro");
EN_LAST_LIST.add("rist");
EN_LAST_LIST.add("mia");
EN_LAST_LIST.add("ry");
EN_LAST_LIST.add("mie");
EN_LAST_LIST.add("dair");
EN_LAST_LIST.add("sa");
EN_LAST_LIST.add("se");
EN_LAST_LIST.add("min");
EN_LAST_LIST.add("ken");
EN_LAST_LIST.add("sh");
EN_LAST_LIST.add("belle");
EN_LAST_LIST.add("ian");
EN_LAST_LIST.add("lian");
EN_LAST_LIST.add("fith");
EN_LAST_LIST.add("kes");
EN_LAST_LIST.add("ker");
EN_LAST_LIST.add("sibyl");
EN_LAST_LIST.add("fred");
EN_LAST_LIST.add("liam");
EN_LAST_LIST.add("wolf");
EN_LAST_LIST.add("sy");
EN_LAST_LIST.add("mann");
EN_LAST_LIST.add("lome");
EN_LAST_LIST.add("josh");
EN_LAST_LIST.add("ta");
EN_LAST_LIST.add("flower");
EN_LAST_LIST.add("te");
EN_LAST_LIST.add("hill");
EN_LAST_LIST.add("stan");
EN_LAST_LIST.add("mand");
EN_LAST_LIST.add("stal");
EN_LAST_LIST.add("to");
EN_LAST_LIST.add("bur");
EN_LAST_LIST.add("dys");
EN_LAST_LIST.add("ty");
EN_LAST_LIST.add("ice");
EN_LAST_LIST.add("woolf");
EN_LAST_LIST.add("jean");
EN_LAST_LIST.add("wood");
EN_LAST_LIST.add("bard");
EN_LAST_LIST.add("zel");
EN_LAST_LIST.add("crane");
EN_LAST_LIST.add("zer");
EN_LAST_LIST.add("va");
EN_LAST_LIST.add("lice");
EN_LAST_LIST.add("ve");
EN_LAST_LIST.add("frey");
EN_LAST_LIST.add("vi");
EN_LAST_LIST.add("wyatt");
EN_LAST_LIST.add("thia");
EN_LAST_LIST.add("sing");
EN_LAST_LIST.add("coln");
EN_LAST_LIST.add("vy");
EN_LAST_LIST.add("colm");
EN_LAST_LIST.add("nold");
EN_LAST_LIST.add("cole");
EN_LAST_LIST.add("dams");
EN_LAST_LIST.add("we");
EN_LAST_LIST.add("jill");
EN_LAST_LIST.add("gai");
EN_LAST_LIST.add("kim");
EN_LAST_LIST.add("kin");
EN_LAST_LIST.add("ien");
EN_LAST_LIST.add("gan");
EN_LAST_LIST.add("kit");
EN_LAST_LIST.add("nolds");
EN_LAST_LIST.add("drow");
EN_LAST_LIST.add("gar");
EN_LAST_LIST.add("liet");
EN_LAST_LIST.add("wy");
EN_LAST_LIST.add("xe");
EN_LAST_LIST.add("bart");
EN_LAST_LIST.add("stone");
EN_LAST_LIST.add("thodore");
EN_LAST_LIST.add("ster");
EN_LAST_LIST.add("mark");
EN_LAST_LIST.add("xy");
EN_LAST_LIST.add("jeff");
EN_LAST_LIST.add("laide");
EN_LAST_LIST.add("jeames");
EN_LAST_LIST.add("ye");
EN_LAST_LIST.add("mon");
EN_LAST_LIST.add("mos");
EN_LAST_LIST.add("maud");
EN_LAST_LIST.add("niah");
EN_LAST_LIST.add("price");
EN_LAST_LIST.add("zie");
EN_LAST_LIST.add("yy");
EN_LAST_LIST.add("van");
EN_LAST_LIST.add("matt");
EN_LAST_LIST.add("keith");
EN_LAST_LIST.add("ze");
EN_LAST_LIST.add("ckey");
EN_LAST_LIST.add("cker");
EN_LAST_LIST.add("zy");
EN_LAST_LIST.add("gee");
EN_LAST_LIST.add("north");
EN_LAST_LIST.add("james");
EN_LAST_LIST.add("claire");
EN_LAST_LIST.add("gel");
EN_LAST_LIST.add("nick");
EN_LAST_LIST.add("gen");
EN_LAST_LIST.add("ges");
EN_LAST_LIST.add("ger");
EN_LAST_LIST.add("kyle");
EN_LAST_LIST.add("morse");
EN_LAST_LIST.add("get");
EN_LAST_LIST.add("tricia");
EN_LAST_LIST.add("wilde");
EN_LAST_LIST.add("cook");
EN_LAST_LIST.add("sell");
EN_LAST_LIST.add("thune");
EN_LAST_LIST.add("nice");
EN_LAST_LIST.add("pold");
EN_LAST_LIST.add("nore");
EN_LAST_LIST.add("pole");
EN_LAST_LIST.add("tours");
EN_LAST_LIST.add("xia");
EN_LAST_LIST.add("niel");
EN_LAST_LIST.add("tab");
EN_LAST_LIST.add("ven");
EN_LAST_LIST.add("ver");
EN_LAST_LIST.add("lotte");
EN_LAST_LIST.add("vey");
EN_LAST_LIST.add("niei");
EN_LAST_LIST.add("webb");
EN_LAST_LIST.add("cooke");
EN_LAST_LIST.add("gia");
EN_LAST_LIST.add("lind");
EN_LAST_LIST.add("gie");
EN_LAST_LIST.add("dave");
EN_LAST_LIST.add("ruth");
EN_LAST_LIST.add("cott");
EN_LAST_LIST.add("ling");
EN_LAST_LIST.add("line");
EN_LAST_LIST.add("cah");
EN_LAST_LIST.add("gil");
EN_LAST_LIST.add("cam");
EN_LAST_LIST.add("ckle");
EN_LAST_LIST.add("leen");
EN_LAST_LIST.add("can");
EN_LAST_LIST.add("zoe");
EN_LAST_LIST.add("cas");
EN_LAST_LIST.add("car");
EN_LAST_LIST.add("buck");
EN_LAST_LIST.add("wells");
EN_LAST_LIST.add("ine");
EN_LAST_LIST.add("ing");
EN_LAST_LIST.add("will");
EN_LAST_LIST.add("rhys");
EN_LAST_LIST.add("rusk");
EN_LAST_LIST.add("jack");
EN_LAST_LIST.add("ledk");
EN_LAST_LIST.add("stowe");
EN_LAST_LIST.add("york");
EN_LAST_LIST.add("hearst");
EN_LAST_LIST.add("reade");
EN_LAST_LIST.add("loyd");
EN_LAST_LIST.add("wild");
EN_LAST_LIST.add("seph");
EN_LAST_LIST.add("gust");
EN_LAST_LIST.add("sper");
}
public static void initCN_LAST_NAME() {
CN_LAST_NAME.add("怀");
CN_LAST_NAME.add("老");
CN_LAST_NAME.add("堂");
CN_LAST_NAME.add("考");
CN_LAST_NAME.add("太史");
CN_LAST_NAME.add("逄");
CN_LAST_NAME.add("栋");
CN_LAST_NAME.add("闻人");
CN_LAST_NAME.add("树");
CN_LAST_NAME.add("栗");
CN_LAST_NAME.add("候");
CN_LAST_NAME.add("通");
CN_LAST_NAME.add("速");
CN_LAST_NAME.add("校");
CN_LAST_NAME.add("逢");
CN_LAST_NAME.add("性");
CN_LAST_NAME.add("倪");
CN_LAST_NAME.add("逮");
CN_LAST_NAME.add("逯");
CN_LAST_NAME.add("堵");
CN_LAST_NAME.add("栾");
CN_LAST_NAME.add("耿");
CN_LAST_NAME.add("桂");
CN_LAST_NAME.add("聂");
CN_LAST_NAME.add("衅");
CN_LAST_NAME.add("遇");
CN_LAST_NAME.add("聊");
CN_LAST_NAME.add("行");
CN_LAST_NAME.add("桐");
CN_LAST_NAME.add("桑");
CN_LAST_NAME.add("道");
CN_LAST_NAME.add("桓");
CN_LAST_NAME.add("塔");
CN_LAST_NAME.add("硕");
CN_LAST_NAME.add("尤念");
CN_LAST_NAME.add("塞");
CN_LAST_NAME.add("衡");
CN_LAST_NAME.add("衣");
CN_LAST_NAME.add("桥");
CN_LAST_NAME.add("令狐");
CN_LAST_NAME.add("表");
CN_LAST_NAME.add("张简");
CN_LAST_NAME.add("恭");
CN_LAST_NAME.add("偶");
CN_LAST_NAME.add("衷");
CN_LAST_NAME.add("项");
CN_LAST_NAME.add("须");
CN_LAST_NAME.add("恽");
CN_LAST_NAME.add("顾");
CN_LAST_NAME.add("顿");
CN_LAST_NAME.add("梁");
CN_LAST_NAME.add("袁");
CN_LAST_NAME.add("漆雕");
CN_LAST_NAME.add("梅");
CN_LAST_NAME.add("傅");
CN_LAST_NAME.add("肇");
CN_LAST_NAME.add("悉");
CN_LAST_NAME.add("夏侯");
CN_LAST_NAME.add("频");
CN_LAST_NAME.add("邓");
CN_LAST_NAME.add("肖");
CN_LAST_NAME.add("邗");
CN_LAST_NAME.add("邛");
CN_LAST_NAME.add("章佳");
CN_LAST_NAME.add("颜");
CN_LAST_NAME.add("邝");
CN_LAST_NAME.add("悟");
CN_LAST_NAME.add("邢");
CN_LAST_NAME.add("那");
CN_LAST_NAME.add("肥");
CN_LAST_NAME.add("碧");
CN_LAST_NAME.add("储");
CN_LAST_NAME.add("墨");
CN_LAST_NAME.add("邬");
CN_LAST_NAME.add("袭");
CN_LAST_NAME.add("邰");
CN_LAST_NAME.add("邱");
CN_LAST_NAME.add("邴");
CN_LAST_NAME.add("邵");
CN_LAST_NAME.add("碧鲁");
CN_LAST_NAME.add("邶");
CN_LAST_NAME.add("邸");
CN_LAST_NAME.add("邹");
CN_LAST_NAME.add("检");
CN_LAST_NAME.add("郁");
CN_LAST_NAME.add("郎");
CN_LAST_NAME.add("风");
CN_LAST_NAME.add("郏");
CN_LAST_NAME.add("郑");
CN_LAST_NAME.add("裔");
CN_LAST_NAME.add("郗");
CN_LAST_NAME.add("裘");
CN_LAST_NAME.add("郜");
CN_LAST_NAME.add("郝");
CN_LAST_NAME.add("飞");
CN_LAST_NAME.add("烟");
CN_LAST_NAME.add("惠");
CN_LAST_NAME.add("胡");
CN_LAST_NAME.add("胥");
CN_LAST_NAME.add("郦");
CN_LAST_NAME.add("僧");
CN_LAST_NAME.add("第五");
CN_LAST_NAME.add("磨");
CN_LAST_NAME.add("僪");
CN_LAST_NAME.add("由念");
CN_LAST_NAME.add("士");
CN_LAST_NAME.add("壬");
CN_LAST_NAME.add("郭");
CN_LAST_NAME.add("钟离");
CN_LAST_NAME.add("森");
CN_LAST_NAME.add("郯");
CN_LAST_NAME.add("声");
CN_LAST_NAME.add("裴");
CN_LAST_NAME.add("郸");
CN_LAST_NAME.add("都");
CN_LAST_NAME.add("能");
CN_LAST_NAME.add("鄂");
CN_LAST_NAME.add("愈");
CN_LAST_NAME.add("焉");
CN_LAST_NAME.add("植");
CN_LAST_NAME.add("夏");
CN_LAST_NAME.add("褒");
CN_LAST_NAME.add("夔");
CN_LAST_NAME.add("夕");
CN_LAST_NAME.add("夙");
CN_LAST_NAME.add("多");
CN_LAST_NAME.add("褚");
CN_LAST_NAME.add("愚");
CN_LAST_NAME.add("鄞");
CN_LAST_NAME.add("鄢");
CN_LAST_NAME.add("焦");
CN_LAST_NAME.add("大");
CN_LAST_NAME.add("天");
CN_LAST_NAME.add("夫");
CN_LAST_NAME.add("脱");
CN_LAST_NAME.add("夷");
CN_LAST_NAME.add("示");
CN_LAST_NAME.add("礼");
CN_LAST_NAME.add("祁");
CN_LAST_NAME.add("允");
CN_LAST_NAME.add("元");
CN_LAST_NAME.add("充");
CN_LAST_NAME.add("兆");
CN_LAST_NAME.add("酆");
CN_LAST_NAME.add("奇");
CN_LAST_NAME.add("祈");
CN_LAST_NAME.add("慈");
CN_LAST_NAME.add("奈");
CN_LAST_NAME.add("奉");
CN_LAST_NAME.add("光");
CN_LAST_NAME.add("慎");
CN_LAST_NAME.add("段干");
CN_LAST_NAME.add("酒");
CN_LAST_NAME.add("慕");
CN_LAST_NAME.add("奕");
CN_LAST_NAME.add("祖");
CN_LAST_NAME.add("党");
CN_LAST_NAME.add("楚");
CN_LAST_NAME.add("奚");
CN_LAST_NAME.add("祝");
CN_LAST_NAME.add("祢");
CN_LAST_NAME.add("但念");
CN_LAST_NAME.add("全");
CN_LAST_NAME.add("公");
CN_LAST_NAME.add("六");
CN_LAST_NAME.add("祭");
CN_LAST_NAME.add("兰");
CN_LAST_NAME.add("关");
CN_LAST_NAME.add("兴");
CN_LAST_NAME.add("其");
CN_LAST_NAME.add("饶");
CN_LAST_NAME.add("典");
CN_LAST_NAME.add("养");
CN_LAST_NAME.add("楼");
CN_LAST_NAME.add("腾");
CN_LAST_NAME.add("冀");
CN_LAST_NAME.add("覃");
CN_LAST_NAME.add("禄");
CN_LAST_NAME.add("冉");
CN_LAST_NAME.add("熊");
CN_LAST_NAME.add("福");
CN_LAST_NAME.add("冒");
CN_LAST_NAME.add("首");
CN_LAST_NAME.add("富察");
CN_LAST_NAME.add("香");
CN_LAST_NAME.add("禚");
CN_LAST_NAME.add("军");
CN_LAST_NAME.add("农");
CN_LAST_NAME.add("冠");
CN_LAST_NAME.add("漆念");
CN_LAST_NAME.add("妫");
CN_LAST_NAME.add("冯");
CN_LAST_NAME.add("况");
CN_LAST_NAME.add("冷");
CN_LAST_NAME.add("禹");
CN_LAST_NAME.add("冼");
CN_LAST_NAME.add("禽");
CN_LAST_NAME.add("禾");
CN_LAST_NAME.add("释");
CN_LAST_NAME.add("秋");
CN_LAST_NAME.add("始");
CN_LAST_NAME.add("凌");
CN_LAST_NAME.add("种");
CN_LAST_NAME.add("野");
CN_LAST_NAME.add("金");
CN_LAST_NAME.add("姒");
CN_LAST_NAME.add("姓");
CN_LAST_NAME.add("委");
CN_LAST_NAME.add("燕");
CN_LAST_NAME.add("秘");
CN_LAST_NAME.add("姚");
CN_LAST_NAME.add("姜");
CN_LAST_NAME.add("解");
CN_LAST_NAME.add("凤");
CN_LAST_NAME.add("秦");
CN_LAST_NAME.add("臧");
CN_LAST_NAME.add("巫马");
CN_LAST_NAME.add("姬");
CN_LAST_NAME.add("凭");
CN_LAST_NAME.add("称");
CN_LAST_NAME.add("呼延");
CN_LAST_NAME.add("乌雅");
CN_LAST_NAME.add("出");
CN_LAST_NAME.add("函");
CN_LAST_NAME.add("言");
CN_LAST_NAME.add("刀");
CN_LAST_NAME.add("刁");
CN_LAST_NAME.add("威");
CN_LAST_NAME.add("娄");
CN_LAST_NAME.add("戈");
CN_LAST_NAME.add("樊");
CN_LAST_NAME.add("戊");
CN_LAST_NAME.add("程");
CN_LAST_NAME.add("戎");
CN_LAST_NAME.add("税");
CN_LAST_NAME.add("戏");
CN_LAST_NAME.add("成");
CN_LAST_NAME.add("刑");
CN_LAST_NAME.add("舒");
CN_LAST_NAME.add("夹谷");
CN_LAST_NAME.add("端木");
CN_LAST_NAME.add("刘");
CN_LAST_NAME.add("战");
CN_LAST_NAME.add("戚");
CN_LAST_NAME.add("刚");
CN_LAST_NAME.add("舜");
CN_LAST_NAME.add("初");
CN_LAST_NAME.add("戢");
CN_LAST_NAME.add("利");
CN_LAST_NAME.add("别");
CN_LAST_NAME.add("爱");
CN_LAST_NAME.add("戴");
CN_LAST_NAME.add("户");
CN_LAST_NAME.add("稽");
CN_LAST_NAME.add("訾");
CN_LAST_NAME.add("房");
CN_LAST_NAME.add("所");
CN_LAST_NAME.add("穆");
CN_LAST_NAME.add("扈");
CN_LAST_NAME.add("前");
CN_LAST_NAME.add("才");
CN_LAST_NAME.add("剑");
CN_LAST_NAME.add("牛");
CN_LAST_NAME.add("牟");
CN_LAST_NAME.add("牢");
CN_LAST_NAME.add("剧");
CN_LAST_NAME.add("牧");
CN_LAST_NAME.add("马");
CN_LAST_NAME.add("扬");
CN_LAST_NAME.add("良");
CN_LAST_NAME.add("穰");
CN_LAST_NAME.add("牵");
CN_LAST_NAME.add("扶");
CN_LAST_NAME.add("驹");
CN_LAST_NAME.add("詹");
CN_LAST_NAME.add("空");
CN_LAST_NAME.add("艾");
CN_LAST_NAME.add("承");
CN_LAST_NAME.add("檀");
CN_LAST_NAME.add("犁");
CN_LAST_NAME.add("节");
CN_LAST_NAME.add("抄");
CN_LAST_NAME.add("骆");
CN_LAST_NAME.add("司徒");
CN_LAST_NAME.add("骑");
CN_LAST_NAME.add("芒");
CN_LAST_NAME.add("马佳");
CN_LAST_NAME.add("抗");
CN_LAST_NAME.add("折");
CN_LAST_NAME.add("力");
CN_LAST_NAME.add("功");
CN_LAST_NAME.add("务");
CN_LAST_NAME.add("窦");
CN_LAST_NAME.add("芮");
CN_LAST_NAME.add("仲孙");
CN_LAST_NAME.add("励");
CN_LAST_NAME.add("花");
CN_LAST_NAME.add("万俟");
CN_LAST_NAME.add("劳");
CN_LAST_NAME.add("犹");
CN_LAST_NAME.add("势");
CN_LAST_NAME.add("狂");
CN_LAST_NAME.add("狄");
CN_LAST_NAME.add("勇");
CN_LAST_NAME.add("苌");
CN_LAST_NAME.add("苍");
CN_LAST_NAME.add("苏");
CN_LAST_NAME.add("苑");
CN_LAST_NAME.add("苗");
CN_LAST_NAME.add("高");
CN_LAST_NAME.add("招");
CN_LAST_NAME.add("拜");
CN_LAST_NAME.add("苟");
CN_LAST_NAME.add("章");
CN_LAST_NAME.add("勤");
CN_LAST_NAME.add("童");
CN_LAST_NAME.add("苦");
CN_LAST_NAME.add("宇文");
CN_LAST_NAME.add("独");
CN_LAST_NAME.add("竭");
CN_LAST_NAME.add("端");
CN_LAST_NAME.add("拱");
CN_LAST_NAME.add("英");
CN_LAST_NAME.add("竹");
CN_LAST_NAME.add("竺");
CN_LAST_NAME.add("勾");
CN_LAST_NAME.add("百里");
CN_LAST_NAME.add("茂");
CN_LAST_NAME.add("范");
CN_LAST_NAME.add("笃");
CN_LAST_NAME.add("包");
CN_LAST_NAME.add("茅");
CN_LAST_NAME.add("茆");
CN_LAST_NAME.add("謇");
CN_LAST_NAME.add("东方");
CN_LAST_NAME.add("化");
CN_LAST_NAME.add("北");
CN_LAST_NAME.add("次");
CN_LAST_NAME.add("匡");
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CN_LAST_NAME.add("欧");
CN_LAST_NAME.add("笪");
CN_LAST_NAME.add("第");
CN_LAST_NAME.add("嬴");
CN_LAST_NAME.add("茹");
CN_LAST_NAME.add("区");
CN_LAST_NAME.add("谷梁");
CN_LAST_NAME.add("微生");
CN_LAST_NAME.add("南宫");
CN_LAST_NAME.add("荀");
CN_LAST_NAME.add("千");
CN_LAST_NAME.add("东门");
CN_LAST_NAME.add("荆");
CN_LAST_NAME.add("华");
CN_LAST_NAME.add("魏");
CN_LAST_NAME.add("卑");
CN_LAST_NAME.add("卓");
CN_LAST_NAME.add("答");
CN_LAST_NAME.add("孔");
CN_LAST_NAME.add("单");
CN_LAST_NAME.add("字");
CN_LAST_NAME.add("南");
CN_LAST_NAME.add("孙");
CN_LAST_NAME.add("澹台");
CN_LAST_NAME.add("孛");
CN_LAST_NAME.add("卜");
CN_LAST_NAME.add("孝");
CN_LAST_NAME.add("卞");
CN_LAST_NAME.add("孟");
CN_LAST_NAME.add("占");
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CN_LAST_NAME.add("卢");
CN_LAST_NAME.add("荣");
CN_LAST_NAME.add("季");
CN_LAST_NAME.add("荤");
CN_LAST_NAME.add("步");
CN_LAST_NAME.add("学");
CN_LAST_NAME.add("武");
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CN_LAST_NAME.add("卫");
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CN_LAST_NAME.add("印");
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CN_LAST_NAME.add("捷");
CN_LAST_NAME.add("卿");
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CN_LAST_NAME.add("宁");
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CN_LAST_NAME.add("历");
CN_LAST_NAME.add("宇");
CN_LAST_NAME.add("守");
CN_LAST_NAME.add("安");
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CN_LAST_NAME.add("掌");
CN_LAST_NAME.add("完");
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CN_LAST_NAME.add("莘");
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CN_LAST_NAME.add("诸");
CN_LAST_NAME.add("司");
CN_LAST_NAME.add("诺");
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CN_LAST_NAME.add("理");
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CN_LAST_NAME.add("虎");
CN_LAST_NAME.add("晏");
CN_LAST_NAME.add("乐");
CN_LAST_NAME.add("乔");
CN_LAST_NAME.add("乘");
CN_LAST_NAME.add("乙");
CN_LAST_NAME.add("东郭");
CN_LAST_NAME.add("湛");
CN_LAST_NAME.add("乜");
CN_LAST_NAME.add("九");
CN_LAST_NAME.add("虞");
CN_LAST_NAME.add("习");
CN_LAST_NAME.add("虢");
CN_LAST_NAME.add("书");
CN_LAST_NAME.add("普");
CN_LAST_NAME.add("景");
CN_LAST_NAME.add("买");
CN_LAST_NAME.add("干");
CN_LAST_NAME.add("平");
CN_LAST_NAME.add("年");
CN_LAST_NAME.add("陶");
CN_LAST_NAME.add("幸");
CN_LAST_NAME.add("智");
CN_LAST_NAME.add("登");
CN_LAST_NAME.add("白");
CN_LAST_NAME.add("百");
CN_LAST_NAME.add("乾");
CN_LAST_NAME.add("鹿");
CN_LAST_NAME.add("广");
CN_LAST_NAME.add("蚁");
CN_LAST_NAME.add("乌孙");
CN_LAST_NAME.add("庄");
CN_LAST_NAME.add("隆");
CN_LAST_NAME.add("庆");
CN_LAST_NAME.add("皇");
CN_LAST_NAME.add("公良");
CN_LAST_NAME.add("皋");
CN_LAST_NAME.add("隋");
CN_LAST_NAME.add("柴念");
CN_LAST_NAME.add("于");
CN_LAST_NAME.add("随");
CN_LAST_NAME.add("源");
CN_LAST_NAME.add("隐");
CN_LAST_NAME.add("云");
CN_LAST_NAME.add("库");
CN_LAST_NAME.add("亓");
CN_LAST_NAME.add("应");
CN_LAST_NAME.add("五");
CN_LAST_NAME.add("井");
CN_LAST_NAME.add("隗");
CN_LAST_NAME.add("那拉");
CN_LAST_NAME.add("庚");
CN_LAST_NAME.add("完颜");
CN_LAST_NAME.add("府");
CN_LAST_NAME.add("庞");
CN_LAST_NAME.add("图门");
CN_LAST_NAME.add("红");
CN_LAST_NAME.add("亢");
CN_LAST_NAME.add("溥");
CN_LAST_NAME.add("亥");
CN_LAST_NAME.add("度");
CN_LAST_NAME.add("麦");
CN_LAST_NAME.add("暨");
CN_LAST_NAME.add("纪");
CN_LAST_NAME.add("京");
CN_LAST_NAME.add("皮");
CN_LAST_NAME.add("纳");
CN_LAST_NAME.add("暴");
CN_LAST_NAME.add("麴");
CN_LAST_NAME.add("纵");
CN_LAST_NAME.add("康");
CN_LAST_NAME.add("庹");
CN_LAST_NAME.add("麻");
CN_LAST_NAME.add("隽");
CN_LAST_NAME.add("庾");
CN_LAST_NAME.add("线");
CN_LAST_NAME.add("雀");
CN_LAST_NAME.add("仁");
CN_LAST_NAME.add("练");
CN_LAST_NAME.add("黄");
CN_LAST_NAME.add("司寇");
CN_LAST_NAME.add("仆");
CN_LAST_NAME.add("集");
CN_LAST_NAME.add("仇");
CN_LAST_NAME.add("上官");
CN_LAST_NAME.add("盈");
CN_LAST_NAME.add("终");
CN_LAST_NAME.add("廉");
CN_LAST_NAME.add("仉");
CN_LAST_NAME.add("益");
CN_LAST_NAME.add("介");
CN_LAST_NAME.add("盍");
CN_LAST_NAME.add("绍");
CN_LAST_NAME.add("雍");
CN_LAST_NAME.add("仍");
CN_LAST_NAME.add("从");
CN_LAST_NAME.add("黎");
CN_LAST_NAME.add("经");
CN_LAST_NAME.add("滑");
CN_LAST_NAME.add("滕");
CN_LAST_NAME.add("盖");
CN_LAST_NAME.add("廖");
CN_LAST_NAME.add("盘");
CN_LAST_NAME.add("仙");
CN_LAST_NAME.add("盛");
CN_LAST_NAME.add("仝");
CN_LAST_NAME.add("回");
CN_LAST_NAME.add("满");
CN_LAST_NAME.add("代");
CN_LAST_NAME.add("令");
CN_LAST_NAME.add("以");
CN_LAST_NAME.add("绪");
CN_LAST_NAME.add("雪");
CN_LAST_NAME.add("仪");
CN_LAST_NAME.add("续");
CN_LAST_NAME.add("蛮");
CN_LAST_NAME.add("仰");
CN_LAST_NAME.add("仲");
CN_LAST_NAME.add("曲");
CN_LAST_NAME.add("绳");
CN_LAST_NAME.add("仵");
CN_LAST_NAME.add("淳于");
CN_LAST_NAME.add("延");
CN_LAST_NAME.add("零");
CN_LAST_NAME.add("雷");
CN_LAST_NAME.add("相");
CN_LAST_NAME.add("曹");
CN_LAST_NAME.add("建");
CN_LAST_NAME.add("任");
CN_LAST_NAME.add("国");
CN_LAST_NAME.add("曾");
CN_LAST_NAME.add("开");
CN_LAST_NAME.add("漆");
CN_LAST_NAME.add("有");
CN_LAST_NAME.add("伊");
CN_LAST_NAME.add("朋");
CN_LAST_NAME.add("霍");
CN_LAST_NAME.add("伍");
CN_LAST_NAME.add("伏");
CN_LAST_NAME.add("缑");
CN_LAST_NAME.add("休");
CN_LAST_NAME.add("弓");
CN_LAST_NAME.add("弘");
CN_LAST_NAME.add("乐正");
CN_LAST_NAME.add("望");
CN_LAST_NAME.add("霜");
CN_LAST_NAME.add("伟");
CN_LAST_NAME.add("真");
CN_LAST_NAME.add("张");
CN_LAST_NAME.add("圣");
CN_LAST_NAME.add("弥");
CN_LAST_NAME.add("伦");
CN_LAST_NAME.add("在");
CN_LAST_NAME.add("范姜");
CN_LAST_NAME.add("缪");
CN_LAST_NAME.add("漫");
CN_LAST_NAME.add("本");
CN_LAST_NAME.add("圭");
CN_LAST_NAME.add("弭");
CN_LAST_NAME.add("眭");
CN_LAST_NAME.add("伯");
CN_LAST_NAME.add("朱");
CN_LAST_NAME.add("朴");
CN_LAST_NAME.add("强");
CN_LAST_NAME.add("机");
CN_LAST_NAME.add("似");
CN_LAST_NAME.add("权");
CN_LAST_NAME.add("但");
CN_LAST_NAME.add("位");
CN_LAST_NAME.add("李");
CN_LAST_NAME.add("齐");
CN_LAST_NAME.add("归");
CN_LAST_NAME.add("青");
CN_LAST_NAME.add("何");
CN_LAST_NAME.add("罕");
CN_LAST_NAME.add("靖");
CN_LAST_NAME.add("罗");
CN_LAST_NAME.add("潘");
CN_LAST_NAME.add("佘");
CN_LAST_NAME.add("余");
CN_LAST_NAME.add("坚");
CN_LAST_NAME.add("佛");
CN_LAST_NAME.add("潜");
CN_LAST_NAME.add("杜");
CN_LAST_NAME.add("杞");
CN_LAST_NAME.add("佟");
CN_LAST_NAME.add("束");
CN_LAST_NAME.add("睢");
CN_LAST_NAME.add("督");
CN_LAST_NAME.add("彤");
CN_LAST_NAME.add("来");
CN_LAST_NAME.add("车");
CN_LAST_NAME.add("睦");
CN_LAST_NAME.add("公孙");
CN_LAST_NAME.add("杨");
CN_LAST_NAME.add("革");
CN_LAST_NAME.add("亓官");
CN_LAST_NAME.add("彭");
CN_LAST_NAME.add("潭");
CN_LAST_NAME.add("杭");
CN_LAST_NAME.add("潮");
CN_LAST_NAME.add("诸葛");
CN_LAST_NAME.add("靳");
CN_LAST_NAME.add("佴");
CN_LAST_NAME.add("佼");
CN_LAST_NAME.add("载");
CN_LAST_NAME.add("松");
CN_LAST_NAME.add("板");
CN_LAST_NAME.add("澄");
CN_LAST_NAME.add("辉");
CN_LAST_NAME.add("皇甫");
CN_LAST_NAME.add("羊");
CN_LAST_NAME.add("律");
CN_LAST_NAME.add("融");
CN_LAST_NAME.add("侍");
CN_LAST_NAME.add("徐");
CN_LAST_NAME.add("析");
CN_LAST_NAME.add("林");
CN_LAST_NAME.add("龙");
CN_LAST_NAME.add("枚");
CN_LAST_NAME.add("龚");
CN_LAST_NAME.add("辛");
CN_LAST_NAME.add("辜");
CN_LAST_NAME.add("果");
CN_LAST_NAME.add("枝");
CN_LAST_NAME.add("依");
CN_LAST_NAME.add("辟");
CN_LAST_NAME.add("鞠");
CN_LAST_NAME.add("御");
CN_LAST_NAME.add("侨");
CN_LAST_NAME.add("徭");
CN_LAST_NAME.add("侯");
CN_LAST_NAME.add("德");
CN_LAST_NAME.add("边");
CN_LAST_NAME.add("羽");
CN_LAST_NAME.add("达");
CN_LAST_NAME.add("羿");
CN_LAST_NAME.add("瞿");
CN_LAST_NAME.add("翁");
CN_LAST_NAME.add("赫连");
CN_LAST_NAME.add("过");
CN_LAST_NAME.add("闾丘");
CN_LAST_NAME.add("城");
CN_LAST_NAME.add("俎");
CN_LAST_NAME.add("柏");
CN_LAST_NAME.add("运");
CN_LAST_NAME.add("柔");
CN_LAST_NAME.add("进");
CN_LAST_NAME.add("保");
CN_LAST_NAME.add("俞");
CN_LAST_NAME.add("连");
CN_LAST_NAME.add("俟");
CN_LAST_NAME.add("迟");
CN_LAST_NAME.add("翟");
CN_LAST_NAME.add("翠");
CN_LAST_NAME.add("太叔");
CN_LAST_NAME.add("信");
CN_LAST_NAME.add("欧阳");
CN_LAST_NAME.add("公叔");
CN_LAST_NAME.add("查");
CN_LAST_NAME.add("韦");
CN_LAST_NAME.add("翦");
CN_LAST_NAME.add("韩");
CN_LAST_NAME.add("矫");
CN_LAST_NAME.add("濮");
CN_LAST_NAME.add("修");
CN_LAST_NAME.add("迮");
CN_LAST_NAME.add("柯");
CN_LAST_NAME.add("濯");
CN_LAST_NAME.add("柳");
CN_LAST_NAME.add("石");
CN_LAST_NAME.add("柴");
CN_LAST_NAME.add("念");
CN_LAST_NAME.add("韶");
CN_LAST_NAME.add("忻");
}
public static void initCN_FIRST_NAME() {
CN_FIRST_NAME.add("慕雁");
CN_FIRST_NAME.add("婉然");
CN_FIRST_NAME.add("月明");
CN_FIRST_NAME.add("觅儿");
CN_FIRST_NAME.add("高翰");
CN_FIRST_NAME.add("白曼");
CN_FIRST_NAME.add("怀思");
CN_FIRST_NAME.add("碧菡");
CN_FIRST_NAME.add("奇邃");
CN_FIRST_NAME.add("云岚");
CN_FIRST_NAME.add("惜文");
CN_FIRST_NAME.add("夏青");
CN_FIRST_NAME.add("俊雄");
CN_FIRST_NAME.add("俊雅");
CN_FIRST_NAME.add("馨蓉");
CN_FIRST_NAME.add("庄丽");
CN_FIRST_NAME.add("笛韵");
CN_FIRST_NAME.add("笑天");
CN_FIRST_NAME.add("舒怀");
CN_FIRST_NAME.add("梦琪");
CN_FIRST_NAME.add("清润");
CN_FIRST_NAME.add("萦心");
CN_FIRST_NAME.add("丹蝶");
CN_FIRST_NAME.add("长旭");
CN_FIRST_NAME.add("清涵");
CN_FIRST_NAME.add("方仪");
CN_FIRST_NAME.add("杰秀");
CN_FIRST_NAME.add("天瑞");
CN_FIRST_NAME.add("美丽");
CN_FIRST_NAME.add("清淑");
CN_FIRST_NAME.add("忻愉");
CN_FIRST_NAME.add("隽美");
CN_FIRST_NAME.add("碧萱");
CN_FIRST_NAME.add("淑君");
CN_FIRST_NAME.add("诗兰");
CN_FIRST_NAME.add("平灵");
CN_FIRST_NAME.add("柔淑");
CN_FIRST_NAME.add("晓山");
CN_FIRST_NAME.add("乐蓉");
CN_FIRST_NAME.add("良哲");
CN_FIRST_NAME.add("永新");
CN_FIRST_NAME.add("凡阳");
CN_FIRST_NAME.add("莹洁");
CN_FIRST_NAME.add("哲圣");
CN_FIRST_NAME.add("同化");
CN_FIRST_NAME.add("玉英");
CN_FIRST_NAME.add("天和");
CN_FIRST_NAME.add("萦怀");
CN_FIRST_NAME.add("伟毅");
CN_FIRST_NAME.add("凝雁");
CN_FIRST_NAME.add("炎彬");
CN_FIRST_NAME.add("伟诚");
CN_FIRST_NAME.add("长星");
CN_FIRST_NAME.add("笑妍");
CN_FIRST_NAME.add("瀚海");
CN_FIRST_NAME.add("清一");
CN_FIRST_NAME.add("景天");
CN_FIRST_NAME.add("信瑞");
CN_FIRST_NAME.add("鸿雪");
CN_FIRST_NAME.add("子凡");
CN_FIRST_NAME.add("古韵");
CN_FIRST_NAME.add("志文");
CN_FIRST_NAME.add("凝雨");
CN_FIRST_NAME.add("凝雪");
CN_FIRST_NAME.add("萦思");
CN_FIRST_NAME.add("阳炎");
CN_FIRST_NAME.add("忆枫");
CN_FIRST_NAME.add("波光");
CN_FIRST_NAME.add("吉玉");
CN_FIRST_NAME.add("致萱");
CN_FIRST_NAME.add("博裕");
CN_FIRST_NAME.add("秀艾");
CN_FIRST_NAME.add("问风");
CN_FIRST_NAME.add("志新");
CN_FIRST_NAME.add("凡白");
CN_FIRST_NAME.add("忻慕");
CN_FIRST_NAME.add("正德");
CN_FIRST_NAME.add("芳泽");
CN_FIRST_NAME.add("吉玟");
CN_FIRST_NAME.add("秀艳");
CN_FIRST_NAME.add("芳洁");
CN_FIRST_NAME.add("白枫");
CN_FIRST_NAME.add("昆明");
CN_FIRST_NAME.add("忆柏");
CN_FIRST_NAME.add("辰骏");
CN_FIRST_NAME.add("水晶");
CN_FIRST_NAME.add("芳洲");
CN_FIRST_NAME.add("代卉");
CN_FIRST_NAME.add("菡梅");
CN_FIRST_NAME.add("正志");
CN_FIRST_NAME.add("琳溪");
CN_FIRST_NAME.add("叶嘉");
CN_FIRST_NAME.add("永昌");
CN_FIRST_NAME.add("曼衍");
CN_FIRST_NAME.add("书艺");
CN_FIRST_NAME.add("冰岚");
CN_FIRST_NAME.add("永春");
CN_FIRST_NAME.add("梅风");
CN_FIRST_NAME.add("柔丽");
CN_FIRST_NAME.add("元槐");
CN_FIRST_NAME.add("安歌");
CN_FIRST_NAME.add("子爱");
CN_FIRST_NAME.add("融雪");
CN_FIRST_NAME.add("涵韵");
CN_FIRST_NAME.add("香蝶");
CN_FIRST_NAME.add("倩语");
CN_FIRST_NAME.add("乐蕊");
CN_FIRST_NAME.add("康裕");
CN_FIRST_NAME.add("梓露");
CN_FIRST_NAME.add("昕葳");
CN_FIRST_NAME.add("问夏");
CN_FIRST_NAME.add("良畴");
CN_FIRST_NAME.add("毅君");
CN_FIRST_NAME.add("白柏");
CN_FIRST_NAME.add("彭勃");
CN_FIRST_NAME.add("迎真");
CN_FIRST_NAME.add("恨瑶");
CN_FIRST_NAME.add("月朗");
CN_FIRST_NAME.add("雨竹");
CN_FIRST_NAME.add("曼梅");
CN_FIRST_NAME.add("凡雁");
CN_FIRST_NAME.add("景福");
CN_FIRST_NAME.add("代玉");
CN_FIRST_NAME.add("碧蓉");
CN_FIRST_NAME.add("妙松");
CN_FIRST_NAME.add("童彤");
CN_FIRST_NAME.add("浩慨");
CN_FIRST_NAME.add("黎明");
CN_FIRST_NAME.add("黎昕");
CN_FIRST_NAME.add("友安");
CN_FIRST_NAME.add("驰海");
CN_FIRST_NAME.add("凝静");
CN_FIRST_NAME.add("飞鸣");
CN_FIRST_NAME.add("正思");
CN_FIRST_NAME.add("亦竹");
CN_FIRST_NAME.add("运盛");
CN_FIRST_NAME.add("易蓉");
CN_FIRST_NAME.add("芷波");
CN_FIRST_NAME.add("以南");
CN_FIRST_NAME.add("志明");
CN_FIRST_NAME.add("傲安");
CN_FIRST_NAME.add("蔓菁");
CN_FIRST_NAME.add("飞鹏");
CN_FIRST_NAME.add("春芳");
CN_FIRST_NAME.add("新烟");
CN_FIRST_NAME.add("绍晖");
CN_FIRST_NAME.add("凯唱");
CN_FIRST_NAME.add("振平");
CN_FIRST_NAME.add("雅彤");
CN_FIRST_NAME.add("虹颖");
CN_FIRST_NAME.add("从阳");
CN_FIRST_NAME.add("飞鸿");
CN_FIRST_NAME.add("飞鸾");
CN_FIRST_NAME.add("胤文");
CN_FIRST_NAME.add("帅红");
CN_FIRST_NAME.add("秀英");
CN_FIRST_NAME.add("代双");
CN_FIRST_NAME.add("芳润");
CN_FIRST_NAME.add("萱彤");
CN_FIRST_NAME.add("友容");
CN_FIRST_NAME.add("香柏");
CN_FIRST_NAME.add("夜雪");
CN_FIRST_NAME.add("凌香");
CN_FIRST_NAME.add("寻巧");
CN_FIRST_NAME.add("昊明");
CN_FIRST_NAME.add("莞然");
CN_FIRST_NAME.add("绮艳");
CN_FIRST_NAME.add("紫夏");
CN_FIRST_NAME.add("阳焱");
CN_FIRST_NAME.add("昊昊");
CN_FIRST_NAME.add("淑哲");
CN_FIRST_NAME.add("代珊");
CN_FIRST_NAME.add("月杉");
CN_FIRST_NAME.add("宜楠");
CN_FIRST_NAME.add("凡霜");
CN_FIRST_NAME.add("向卉");
CN_FIRST_NAME.add("今雨");
CN_FIRST_NAME.add("彦珺");
CN_FIRST_NAME.add("宵晨");
CN_FIRST_NAME.add("怀慕");
CN_FIRST_NAME.add("姝美");
CN_FIRST_NAME.add("合瑞");
CN_FIRST_NAME.add("妙柏");
CN_FIRST_NAME.add("芮丽");
CN_FIRST_NAME.add("春英");
CN_FIRST_NAME.add("白桃");
CN_FIRST_NAME.add("晋鹏");
CN_FIRST_NAME.add("锦凡");
CN_FIRST_NAME.add("香柳");
CN_FIRST_NAME.add("雨筠");
CN_FIRST_NAME.add("向南");
CN_FIRST_NAME.add("洋洋");
CN_FIRST_NAME.add("静涵");
CN_FIRST_NAME.add("尔竹");
CN_FIRST_NAME.add("献仪");
CN_FIRST_NAME.add("忆梅");
CN_FIRST_NAME.add("自明");
CN_FIRST_NAME.add("若枫");
CN_FIRST_NAME.add("问香");
CN_FIRST_NAME.add("雅美");
CN_FIRST_NAME.add("昭懿");
CN_FIRST_NAME.add("彦君");
CN_FIRST_NAME.add("阳煦");
CN_FIRST_NAME.add("小宸");
CN_FIRST_NAME.add("新儿");
CN_FIRST_NAME.add("青亦");
CN_FIRST_NAME.add("静淑");
CN_FIRST_NAME.add("娅童");
CN_FIRST_NAME.add("寄蓉");
CN_FIRST_NAME.add("阳兰");
CN_FIRST_NAME.add("以珊");
CN_FIRST_NAME.add("寄蓝");
CN_FIRST_NAME.add("明旭");
CN_FIRST_NAME.add("盼夏");
CN_FIRST_NAME.add("含灵");
CN_FIRST_NAME.add("雅志");
CN_FIRST_NAME.add("昂杰");
CN_FIRST_NAME.add("安民");
CN_FIRST_NAME.add("白梅");
CN_FIRST_NAME.add("熙怡");
CN_FIRST_NAME.add("靖之");
CN_FIRST_NAME.add("茉莉");
CN_FIRST_NAME.add("雨安");
CN_FIRST_NAME.add("伟泽");
CN_FIRST_NAME.add("琴轩");
CN_FIRST_NAME.add("倚云");
CN_FIRST_NAME.add("星菱");
CN_FIRST_NAME.add("平凡");
CN_FIRST_NAME.add("丁辰");
CN_FIRST_NAME.add("辰宇");
CN_FIRST_NAME.add("白梦");
CN_FIRST_NAME.add("清漪");
CN_FIRST_NAME.add("熠彤");
CN_FIRST_NAME.add("明明");
CN_FIRST_NAME.add("映菡");
CN_FIRST_NAME.add("阳冰");
CN_FIRST_NAME.add("从雪");
CN_FIRST_NAME.add("易文");
CN_FIRST_NAME.add("香桃");
CN_FIRST_NAME.add("映菱");
CN_FIRST_NAME.add("巍昂");
CN_FIRST_NAME.add("驰丽");
CN_FIRST_NAME.add("兰蕙");
CN_FIRST_NAME.add("振强");
CN_FIRST_NAME.add("锐锋");
CN_FIRST_NAME.add("红豆");
CN_FIRST_NAME.add("寒荷");
CN_FIRST_NAME.add("永望");
CN_FIRST_NAME.add("湛蓝");
CN_FIRST_NAME.add("新冬");
CN_FIRST_NAME.add("飞绿");
CN_FIRST_NAME.add("霏霏");
CN_FIRST_NAME.add("宵月");
CN_FIRST_NAME.add("春荷");
CN_FIRST_NAME.add("尔安");
CN_FIRST_NAME.add("清佳");
CN_FIRST_NAME.add("从霜");
CN_FIRST_NAME.add("田然");
CN_FIRST_NAME.add("同和");
CN_FIRST_NAME.add("盼香");
CN_FIRST_NAME.add("静丹");
CN_FIRST_NAME.add("雪容");
CN_FIRST_NAME.add("映萱");
CN_FIRST_NAME.add("宏毅");
CN_FIRST_NAME.add("含烟");
CN_FIRST_NAME.add("香梅");
CN_FIRST_NAME.add("明智");
CN_FIRST_NAME.add("醉芙");
CN_FIRST_NAME.add("昆杰");
CN_FIRST_NAME.add("妙梦");
CN_FIRST_NAME.add("痴香");
CN_FIRST_NAME.add("尔容");
CN_FIRST_NAME.add("从露");
CN_FIRST_NAME.add("幻儿");
CN_FIRST_NAME.add("山灵");
CN_FIRST_NAME.add("笑笑");
CN_FIRST_NAME.add("优乐");
CN_FIRST_NAME.add("寄蕾");
CN_FIRST_NAME.add("令璟");
CN_FIRST_NAME.add("慧雅");
CN_FIRST_NAME.add("高懿");
CN_FIRST_NAME.add("皎月");
CN_FIRST_NAME.add("月桂");
CN_FIRST_NAME.add("月桃");
CN_FIRST_NAME.add("和蔼");
CN_FIRST_NAME.add("芮优");
CN_FIRST_NAME.add("冰巧");
CN_FIRST_NAME.add("韵宁");
CN_FIRST_NAME.add("古香");
CN_FIRST_NAME.add("盼秋");
CN_FIRST_NAME.add("秋芸");
CN_FIRST_NAME.add("谷枫");
CN_FIRST_NAME.add("秋芳");
CN_FIRST_NAME.add("寄文");
CN_FIRST_NAME.add("瀚漠");
CN_FIRST_NAME.add("静云");
CN_FIRST_NAME.add("泰然");
CN_FIRST_NAME.add("俊风");
CN_FIRST_NAME.add("碧春");
CN_FIRST_NAME.add("灵萱");
CN_FIRST_NAME.add("恬畅");
CN_FIRST_NAME.add("英朗");
CN_FIRST_NAME.add("芝兰");
CN_FIRST_NAME.add("悦乐");
CN_FIRST_NAME.add("清俊");
CN_FIRST_NAME.add("飞龙");
CN_FIRST_NAME.add("光誉");
CN_FIRST_NAME.add("鸿飞");
CN_FIRST_NAME.add("梓颖");
CN_FIRST_NAME.add("寻绿");
CN_FIRST_NAME.add("蔓蔓");
CN_FIRST_NAME.add("安波");
CN_FIRST_NAME.add("沛容");
CN_FIRST_NAME.add("子珍");
CN_FIRST_NAME.add("燕妮");
CN_FIRST_NAME.add("巧荷");
CN_FIRST_NAME.add("鸿风");
CN_FIRST_NAME.add("朝旭");
CN_FIRST_NAME.add("听然");
CN_FIRST_NAME.add("书萱");
CN_FIRST_NAME.add("韫素");
CN_FIRST_NAME.add("孤兰");
CN_FIRST_NAME.add("高扬");
CN_FIRST_NAME.add("元武");
CN_FIRST_NAME.add("秋英");
CN_FIRST_NAME.add("元正");
CN_FIRST_NAME.add("舒扬");
CN_FIRST_NAME.add("飞羽");
CN_FIRST_NAME.add("英杰");
CN_FIRST_NAME.add("韶容");
CN_FIRST_NAME.add("君博");
CN_FIRST_NAME.add("芮佳");
CN_FIRST_NAME.add("同甫");
CN_FIRST_NAME.add("桂芝");
CN_FIRST_NAME.add("兴文");
CN_FIRST_NAME.add("飞翔");
CN_FIRST_NAME.add("姝惠");
CN_FIRST_NAME.add("雅惠");
CN_FIRST_NAME.add("芷云");
CN_FIRST_NAME.add("美偲");
CN_FIRST_NAME.add("昕昕");
CN_FIRST_NAME.add("令锋");
CN_FIRST_NAME.add("振翱");
CN_FIRST_NAME.add("耘志");
CN_FIRST_NAME.add("初然");
CN_FIRST_NAME.add("羡丽");
CN_FIRST_NAME.add("怀芹");
CN_FIRST_NAME.add("觅双");
CN_FIRST_NAME.add("觅珍");
CN_FIRST_NAME.add("芮澜");
CN_FIRST_NAME.add("文静");
CN_FIRST_NAME.add("飞翰");
CN_FIRST_NAME.add("诗珊");
CN_FIRST_NAME.add("飞翮");
CN_FIRST_NAME.add("诗双");
CN_FIRST_NAME.add("明朗");
CN_FIRST_NAME.add("高芬");
CN_FIRST_NAME.add("笑容");
CN_FIRST_NAME.add("意致");
CN_FIRST_NAME.add("飞翼");
CN_FIRST_NAME.add("子琪");
CN_FIRST_NAME.add("哲妍");
CN_FIRST_NAME.add("希彤");
CN_FIRST_NAME.add("悦人");
CN_FIRST_NAME.add("华池");
CN_FIRST_NAME.add("皓月");
CN_FIRST_NAME.add("蕴秀");
CN_FIRST_NAME.add("清逸");
CN_FIRST_NAME.add("芸溪");
CN_FIRST_NAME.add("语儿");
CN_FIRST_NAME.add("宁乐");
CN_FIRST_NAME.add("子琳");
CN_FIRST_NAME.add("寄春");
CN_FIRST_NAME.add("驰轩");
CN_FIRST_NAME.add("思彤");
CN_FIRST_NAME.add("笑寒");
CN_FIRST_NAME.add("秋荣");
CN_FIRST_NAME.add("初兰");
CN_FIRST_NAME.add("婉君");
CN_FIRST_NAME.add("嘉石");
CN_FIRST_NAME.add("嘉音");
CN_FIRST_NAME.add("森丽");
CN_FIRST_NAME.add("鸿祯");
CN_FIRST_NAME.add("秋荷");
CN_FIRST_NAME.add("子瑜");
CN_FIRST_NAME.add("迎天");
CN_FIRST_NAME.add("绣文");
CN_FIRST_NAME.add("兴旺");
CN_FIRST_NAME.add("宜欣");
CN_FIRST_NAME.add("梦雨");
CN_FIRST_NAME.add("迎夏");
CN_FIRST_NAME.add("兴昌");
CN_FIRST_NAME.add("翠曼");
CN_FIRST_NAME.add("山兰");
CN_FIRST_NAME.add("浩荡");
CN_FIRST_NAME.add("施然");
CN_FIRST_NAME.add("淑雅");
CN_FIRST_NAME.add("娴雅");
CN_FIRST_NAME.add("燕婉");
CN_FIRST_NAME.add("思美");
CN_FIRST_NAME.add("天真");
CN_FIRST_NAME.add("问筠");
CN_FIRST_NAME.add("烨霖");
CN_FIRST_NAME.add("泰初");
CN_FIRST_NAME.add("和昶");
CN_FIRST_NAME.add("鸿福");
CN_FIRST_NAME.add("乐松");
CN_FIRST_NAME.add("雍恬");
CN_FIRST_NAME.add("明杰");
CN_FIRST_NAME.add("好洁");
CN_FIRST_NAME.add("越彬");
CN_FIRST_NAME.add("锐阵");
CN_FIRST_NAME.add("碧曼");
CN_FIRST_NAME.add("沛山");
CN_FIRST_NAME.add("格菲");
CN_FIRST_NAME.add("子璇");
CN_FIRST_NAME.add("平卉");
CN_FIRST_NAME.add("倩丽");
CN_FIRST_NAME.add("琬凝");
CN_FIRST_NAME.add("文石");
CN_FIRST_NAME.add("梦露");
CN_FIRST_NAME.add("天青");
CN_FIRST_NAME.add("星文");
CN_FIRST_NAME.add("冰绿");
CN_FIRST_NAME.add("娟妍");
CN_FIRST_NAME.add("惜梦");
CN_FIRST_NAME.add("怜翠");
CN_FIRST_NAME.add("秋莲");
CN_FIRST_NAME.add("承嗣");
CN_FIRST_NAME.add("濡霈");
CN_FIRST_NAME.add("奇玮");
CN_FIRST_NAME.add("之桃");
CN_FIRST_NAME.add("德水");
CN_FIRST_NAME.add("建茗");
CN_FIRST_NAME.add("沛岚");
CN_FIRST_NAME.add("妍歌");
CN_FIRST_NAME.add("雪峰");
CN_FIRST_NAME.add("成荫");
CN_FIRST_NAME.add("志行");
CN_FIRST_NAME.add("云心");
CN_FIRST_NAME.add("鸿禧");
CN_FIRST_NAME.add("谷梦");
CN_FIRST_NAME.add("卿月");
CN_FIRST_NAME.add("阳华");
CN_FIRST_NAME.add("和暄");
CN_FIRST_NAME.add("语冰");
CN_FIRST_NAME.add("梓馨");
CN_FIRST_NAME.add("范明");
CN_FIRST_NAME.add("天睿");
CN_FIRST_NAME.add("晓彤");
CN_FIRST_NAME.add("霞雰");
CN_FIRST_NAME.add("秀敏");
CN_FIRST_NAME.add("和暖");
CN_FIRST_NAME.add("舒荣");
CN_FIRST_NAME.add("暄妍");
CN_FIRST_NAME.add("丁兰");
CN_FIRST_NAME.add("夜天");
CN_FIRST_NAME.add("娟秀");
CN_FIRST_NAME.add("娜娜");
CN_FIRST_NAME.add("凌寒");
CN_FIRST_NAME.add("茜茜");
CN_FIRST_NAME.add("兰月");
CN_FIRST_NAME.add("悠逸");
CN_FIRST_NAME.add("语燕");
CN_FIRST_NAME.add("骊泓");
CN_FIRST_NAME.add("依美");
CN_FIRST_NAME.add("昕月");
CN_FIRST_NAME.add("宏浚");
CN_FIRST_NAME.add("叶飞");
CN_FIRST_NAME.add("骊洁");
CN_FIRST_NAME.add("淑静");
CN_FIRST_NAME.add("嘉颖");
CN_FIRST_NAME.add("思怡");
CN_FIRST_NAME.add("轩昂");
CN_FIRST_NAME.add("如波");
CN_FIRST_NAME.add("迎秋");
CN_FIRST_NAME.add("思思");
CN_FIRST_NAME.add("琛瑞");
CN_FIRST_NAME.add("娴静");
CN_FIRST_NAME.add("紫安");
CN_FIRST_NAME.add("恩霈");
CN_FIRST_NAME.add("问寒");
CN_FIRST_NAME.add("恨真");
CN_FIRST_NAME.add("冰彦");
CN_FIRST_NAME.add("怀莲");
CN_FIRST_NAME.add("雅懿");
CN_FIRST_NAME.add("千亦");
CN_FIRST_NAME.add("运馨");
CN_FIRST_NAME.add("依心");
CN_FIRST_NAME.add("恬雅");
CN_FIRST_NAME.add("希恩");
CN_FIRST_NAME.add("俨雅");
CN_FIRST_NAME.add("驰逸");
CN_FIRST_NAME.add("雅致");
CN_FIRST_NAME.add("青烟");
CN_FIRST_NAME.add("翠柏");
CN_FIRST_NAME.add("思恩");
CN_FIRST_NAME.add("天音");
CN_FIRST_NAME.add("思聪");
CN_FIRST_NAME.add("寒蕾");
CN_FIRST_NAME.add("天韵");
CN_FIRST_NAME.add("书文");
CN_FIRST_NAME.add("一凡");
CN_FIRST_NAME.add("雁芙");
CN_FIRST_NAME.add("娟娟");
CN_FIRST_NAME.add("星星");
CN_FIRST_NAME.add("俊驰");
CN_FIRST_NAME.add("静逸");
CN_FIRST_NAME.add("景山");
CN_FIRST_NAME.add("春蕾");
CN_FIRST_NAME.add("夜香");
CN_FIRST_NAME.add("悦远");
CN_FIRST_NAME.add("碧螺");
CN_FIRST_NAME.add("宜民");
CN_FIRST_NAME.add("健柏");
CN_FIRST_NAME.add("慧颖");
CN_FIRST_NAME.add("彤雯");
CN_FIRST_NAME.add("亦巧");
CN_FIRST_NAME.add("文墨");
CN_FIRST_NAME.add("燕子");
CN_FIRST_NAME.add("冰心");
CN_FIRST_NAME.add("翰藻");
CN_FIRST_NAME.add("星晖");
CN_FIRST_NAME.add("柔煦");
CN_FIRST_NAME.add("红云");
CN_FIRST_NAME.add("兴朝");
CN_FIRST_NAME.add("念蕾");
CN_FIRST_NAME.add("国安");
CN_FIRST_NAME.add("睿识");
CN_FIRST_NAME.add("曦之");
CN_FIRST_NAME.add("德泽");
CN_FIRST_NAME.add("鸿骞");
CN_FIRST_NAME.add("雪巧");
CN_FIRST_NAME.add("寄松");
CN_FIRST_NAME.add("睿诚");
CN_FIRST_NAME.add("仙韵");
CN_FIRST_NAME.add("彤霞");
CN_FIRST_NAME.add("星晴");
CN_FIRST_NAME.add("姝艳");
CN_FIRST_NAME.add("又绿");
CN_FIRST_NAME.add("念文");
CN_FIRST_NAME.add("智宇");
CN_FIRST_NAME.add("聪睿");
CN_FIRST_NAME.add("元洲");
CN_FIRST_NAME.add("巧蕊");
CN_FIRST_NAME.add("向阳");
CN_FIRST_NAME.add("梓婷");
CN_FIRST_NAME.add("宏深");
CN_FIRST_NAME.add("欢欣");
CN_FIRST_NAME.add("雪帆");
CN_FIRST_NAME.add("泰华");
CN_FIRST_NAME.add("蔚星");
CN_FIRST_NAME.add("绮文");
CN_FIRST_NAME.add("斯琪");
CN_FIRST_NAME.add("雅艳");
CN_FIRST_NAME.add("恬静");
CN_FIRST_NAME.add("书易");
CN_FIRST_NAME.add("幻玉");
CN_FIRST_NAME.add("谷槐");
CN_FIRST_NAME.add("琦珍");
CN_FIRST_NAME.add("琪华");
CN_FIRST_NAME.add("翠桃");
CN_FIRST_NAME.add("欣欣");
CN_FIRST_NAME.add("平和");
CN_FIRST_NAME.add("智宸");
CN_FIRST_NAME.add("嘉祥");
CN_FIRST_NAME.add("曼语");
CN_FIRST_NAME.add("鹏飞");
CN_FIRST_NAME.add("华清");
CN_FIRST_NAME.add("佳文");
CN_FIRST_NAME.add("暄婷");
CN_FIRST_NAME.add("彦露");
CN_FIRST_NAME.add("夏容");
CN_FIRST_NAME.add("玮艺");
CN_FIRST_NAME.add("心语");
CN_FIRST_NAME.add("嘉祯");
CN_FIRST_NAME.add("令雪");
CN_FIRST_NAME.add("莹然");
CN_FIRST_NAME.add("宏义");
CN_FIRST_NAME.add("孟君");
CN_FIRST_NAME.add("沈思");
CN_FIRST_NAME.add("心诺");
CN_FIRST_NAME.add("寄柔");
CN_FIRST_NAME.add("修雅");
CN_FIRST_NAME.add("茂材");
CN_FIRST_NAME.add("英楠");
CN_FIRST_NAME.add("畅然");
CN_FIRST_NAME.add("听南");
CN_FIRST_NAME.add("敏思");
CN_FIRST_NAME.add("幻珊");
CN_FIRST_NAME.add("夏寒");
CN_FIRST_NAME.add("晨希");
CN_FIRST_NAME.add("鹏天");
CN_FIRST_NAME.add("怡悦");
CN_FIRST_NAME.add("涵容");
CN_FIRST_NAME.add("晴岚");
CN_FIRST_NAME.add("翠梅");
CN_FIRST_NAME.add("嘉福");
CN_FIRST_NAME.add("德海");
CN_FIRST_NAME.add("运骏");
CN_FIRST_NAME.add("含玉");
CN_FIRST_NAME.add("嘉禧");
CN_FIRST_NAME.add("凯风");
CN_FIRST_NAME.add("凝竹");
CN_FIRST_NAME.add("靖儿");
CN_FIRST_NAME.add("学博");
CN_FIRST_NAME.add("梓童");
CN_FIRST_NAME.add("海荣");
CN_FIRST_NAME.add("春晓");
CN_FIRST_NAME.add("希慕");
CN_FIRST_NAME.add("竹悦");
CN_FIRST_NAME.add("德润");
CN_FIRST_NAME.add("雁荷");
CN_FIRST_NAME.add("幼珊");
CN_FIRST_NAME.add("永言");
CN_FIRST_NAME.add("良奥");
CN_FIRST_NAME.add("华乐");
CN_FIRST_NAME.add("新瑶");
CN_FIRST_NAME.add("初南");
CN_FIRST_NAME.add("贝丽");
CN_FIRST_NAME.add("暄嫣");
CN_FIRST_NAME.add("向雁");
CN_FIRST_NAME.add("春晖");
CN_FIRST_NAME.add("心水");
CN_FIRST_NAME.add("甘雨");
CN_FIRST_NAME.add("嘉禾");
CN_FIRST_NAME.add("思慧");
CN_FIRST_NAME.add("烨磊");
CN_FIRST_NAME.add("之槐");
CN_FIRST_NAME.add("向雪");
CN_FIRST_NAME.add("凯复");
CN_FIRST_NAME.add("奇略");
CN_FIRST_NAME.add("修真");
CN_FIRST_NAME.add("访风");
CN_FIRST_NAME.add("端懿");
CN_FIRST_NAME.add("易梦");
CN_FIRST_NAME.add("季同");
CN_FIRST_NAME.add("如之");
CN_FIRST_NAME.add("佩杉");
CN_FIRST_NAME.add("含双");
CN_FIRST_NAME.add("飞舟");
CN_FIRST_NAME.add("康泰");
CN_FIRST_NAME.add("亦绿");
CN_FIRST_NAME.add("逸丽");
CN_FIRST_NAME.add("巧春");
CN_FIRST_NAME.add("芷烟");
CN_FIRST_NAME.add("彩静");
CN_FIRST_NAME.add("宇达");
CN_FIRST_NAME.add("飞航");
CN_FIRST_NAME.add("向真");
CN_FIRST_NAME.add("听双");
CN_FIRST_NAME.add("鸿宝");
CN_FIRST_NAME.add("光济");
CN_FIRST_NAME.add("海莹");
CN_FIRST_NAME.add("曜灿");
CN_FIRST_NAME.add("秀曼");
CN_FIRST_NAME.add("咸英");
CN_FIRST_NAME.add("慧秀");
CN_FIRST_NAME.add("安澜");
CN_FIRST_NAME.add("琨瑜");
CN_FIRST_NAME.add("文姝");
CN_FIRST_NAME.add("兰梦");
CN_FIRST_NAME.add("贤淑");
CN_FIRST_NAME.add("琨瑶");
CN_FIRST_NAME.add("雁菱");
CN_FIRST_NAME.add("如云");
CN_FIRST_NAME.add("珺娅");
CN_FIRST_NAME.add("凝安");
CN_FIRST_NAME.add("海菡");
CN_FIRST_NAME.add("雪绿");
CN_FIRST_NAME.add("逸云");
CN_FIRST_NAME.add("德业");
CN_FIRST_NAME.add("光赫");
CN_FIRST_NAME.add("夏山");
CN_FIRST_NAME.add("绮晴");
CN_FIRST_NAME.add("乃欣");
CN_FIRST_NAME.add("奕叶");
CN_FIRST_NAME.add("向露");
CN_FIRST_NAME.add("博赡");
CN_FIRST_NAME.add("温书");
CN_FIRST_NAME.add("涵山");
CN_FIRST_NAME.add("雁菡");
CN_FIRST_NAME.add("承基");
CN_FIRST_NAME.add("初珍");
CN_FIRST_NAME.add("访天");
CN_FIRST_NAME.add("飞扬");
CN_FIRST_NAME.add("一南");
CN_FIRST_NAME.add("佳晨");
CN_FIRST_NAME.add("夏岚");
CN_FIRST_NAME.add("博超");
CN_FIRST_NAME.add("瑞渊");
CN_FIRST_NAME.add("博涉");
CN_FIRST_NAME.add("恨风");
CN_FIRST_NAME.add("燕岚");
CN_FIRST_NAME.add("邵美");
CN_FIRST_NAME.add("学名");
CN_FIRST_NAME.add("雨彤");
CN_FIRST_NAME.add("天禄");
CN_FIRST_NAME.add("怀蕾");
CN_FIRST_NAME.add("广君");
CN_FIRST_NAME.add("晓慧");
CN_FIRST_NAME.add("德义");
CN_FIRST_NAME.add("成文");
CN_FIRST_NAME.add("宏伟");
CN_FIRST_NAME.add("蒙雨");
CN_FIRST_NAME.add("云臻");
CN_FIRST_NAME.add("洋然");
CN_FIRST_NAME.add("芷兰");
CN_FIRST_NAME.add("琬琰");
CN_FIRST_NAME.add("博涛");
CN_FIRST_NAME.add("宏伯");
CN_FIRST_NAME.add("怀薇");
CN_FIRST_NAME.add("思懿");
CN_FIRST_NAME.add("美华");
CN_FIRST_NAME.add("鹏程");
CN_FIRST_NAME.add("泰和");
CN_FIRST_NAME.add("霞飞");
CN_FIRST_NAME.add("婷然");
CN_FIRST_NAME.add("芸儿");
CN_FIRST_NAME.add("微澜");
CN_FIRST_NAME.add("浩旷");
CN_FIRST_NAME.add("如仪");
CN_FIRST_NAME.add("绿蓉");
CN_FIRST_NAME.add("玉树");
CN_FIRST_NAME.add("灵松");
CN_FIRST_NAME.add("翰林");
CN_FIRST_NAME.add("昭昭");
CN_FIRST_NAME.add("逸仙");
CN_FIRST_NAME.add("慕山");
CN_FIRST_NAME.add("溥心");
CN_FIRST_NAME.add("秋春");
CN_FIRST_NAME.add("醉易");
CN_FIRST_NAME.add("小翠");
CN_FIRST_NAME.add("梦香");
CN_FIRST_NAME.add("秀杰");
CN_FIRST_NAME.add("飞英");
CN_FIRST_NAME.add("元亮");
CN_FIRST_NAME.add("慧婕");
CN_FIRST_NAME.add("旭东");
CN_FIRST_NAME.add("和裕");
CN_FIRST_NAME.add("子真");
CN_FIRST_NAME.add("牧歌");
CN_FIRST_NAME.add("洮洮");
CN_FIRST_NAME.add("弘致");
CN_FIRST_NAME.add("北嘉");
CN_FIRST_NAME.add("灵枫");
CN_FIRST_NAME.add("书蝶");
CN_FIRST_NAME.add("清卓");
CN_FIRST_NAME.add("清华");
CN_FIRST_NAME.add("艳娇");
CN_FIRST_NAME.add("寒松");
CN_FIRST_NAME.add("梦秋");
CN_FIRST_NAME.add("景平");
CN_FIRST_NAME.add("宛丝");
CN_FIRST_NAME.add("弘懿");
CN_FIRST_NAME.add("曜儿");
CN_FIRST_NAME.add("华辉");
CN_FIRST_NAME.add("芸熙");
CN_FIRST_NAME.add("承颜");
CN_FIRST_NAME.add("琰琬");
CN_FIRST_NAME.add("初瑶");
CN_FIRST_NAME.add("敏慧");
CN_FIRST_NAME.add("暮雨");
CN_FIRST_NAME.add("舒方");
CN_FIRST_NAME.add("雅萍");
CN_FIRST_NAME.add("辰龙");
CN_FIRST_NAME.add("瑞云");
CN_FIRST_NAME.add("巧曼");
CN_FIRST_NAME.add("君雅");
CN_FIRST_NAME.add("光临");
CN_FIRST_NAME.add("雪羽");
CN_FIRST_NAME.add("宏达");
CN_FIRST_NAME.add("良骥");
CN_FIRST_NAME.add("采绿");
CN_FIRST_NAME.add("暖姝");
CN_FIRST_NAME.add("骞泽");
CN_FIRST_NAME.add("田田");
CN_FIRST_NAME.add("爰爰");
CN_FIRST_NAME.add("伟兆");
CN_FIRST_NAME.add("良骏");
CN_FIRST_NAME.add("易槐");
CN_FIRST_NAME.add("寻芳");
CN_FIRST_NAME.add("芫华");
CN_FIRST_NAME.add("寻芹");
CN_FIRST_NAME.add("献玉");
CN_FIRST_NAME.add("米琪");
CN_FIRST_NAME.add("振荣");
CN_FIRST_NAME.add("觅露");
CN_FIRST_NAME.add("绣梓");
CN_FIRST_NAME.add("绿蕊");
CN_FIRST_NAME.add("阳嘉");
CN_FIRST_NAME.add("高明");
CN_FIRST_NAME.add("宏远");
CN_FIRST_NAME.add("家欣");
CN_FIRST_NAME.add("博丽");
CN_FIRST_NAME.add("春枫");
CN_FIRST_NAME.add("知慧");
CN_FIRST_NAME.add("高旻");
CN_FIRST_NAME.add("诗霜");
CN_FIRST_NAME.add("安邦");
CN_FIRST_NAME.add("雪翎");
CN_FIRST_NAME.add("高昂");
CN_FIRST_NAME.add("雁蓉");
CN_FIRST_NAME.add("婉静");
CN_FIRST_NAME.add("立果");
CN_FIRST_NAME.add("春柔");
CN_FIRST_NAME.add("春柏");
CN_FIRST_NAME.add("悦爱");
CN_FIRST_NAME.add("意蕴");
CN_FIRST_NAME.add("沙羽");
CN_FIRST_NAME.add("飞荷");
CN_FIRST_NAME.add("韶美");
CN_FIRST_NAME.add("海蓝");
CN_FIRST_NAME.add("飞捷");
CN_FIRST_NAME.add("真如");
CN_FIRST_NAME.add("远骞");
CN_FIRST_NAME.add("千儿");
CN_FIRST_NAME.add("从筠");
CN_FIRST_NAME.add("妍丽");
CN_FIRST_NAME.add("建明");
CN_FIRST_NAME.add("弘扬");
CN_FIRST_NAME.add("宛亦");
CN_FIRST_NAME.add("棠华");
CN_FIRST_NAME.add("骏伟");
CN_FIRST_NAME.add("思若");
CN_FIRST_NAME.add("令飒");
CN_FIRST_NAME.add("盼巧");
CN_FIRST_NAME.add("馨欣");
CN_FIRST_NAME.add("丽泽");
CN_FIRST_NAME.add("霞姝");
CN_FIRST_NAME.add("天骄");
CN_FIRST_NAME.add("德佑");
CN_FIRST_NAME.add("阳阳");
CN_FIRST_NAME.add("从安");
CN_FIRST_NAME.add("康乐");
CN_FIRST_NAME.add("念柏");
CN_FIRST_NAME.add("一瑾");
CN_FIRST_NAME.add("经武");
CN_FIRST_NAME.add("天空");
CN_FIRST_NAME.add("香波");
CN_FIRST_NAME.add("宏逸");
CN_FIRST_NAME.add("英武");
CN_FIRST_NAME.add("承天");
CN_FIRST_NAME.add("琳瑜");
CN_FIRST_NAME.add("飞莲");
CN_FIRST_NAME.add("正文");
CN_FIRST_NAME.add("云英");
CN_FIRST_NAME.add("金鹏");
CN_FIRST_NAME.add("一璇");
CN_FIRST_NAME.add("光亮");
CN_FIRST_NAME.add("秋月");
CN_FIRST_NAME.add("书桃");
CN_FIRST_NAME.add("淑婉");
CN_FIRST_NAME.add("宜人");
CN_FIRST_NAME.add("飞掣");
CN_FIRST_NAME.add("淑穆");
CN_FIRST_NAME.add("天媛");
CN_FIRST_NAME.add("香洁");
CN_FIRST_NAME.add("琼华");
CN_FIRST_NAME.add("娴婉");
CN_FIRST_NAME.add("绿旋");
CN_FIRST_NAME.add("洁玉");
CN_FIRST_NAME.add("莹华");
CN_FIRST_NAME.add("子石");
CN_FIRST_NAME.add("代天");
CN_FIRST_NAME.add("梅红");
CN_FIRST_NAME.add("茵茵");
CN_FIRST_NAME.add("春桃");
CN_FIRST_NAME.add("娅思");
CN_FIRST_NAME.add("思茵");
CN_FIRST_NAME.add("洛灵");
CN_FIRST_NAME.add("平雅");
CN_FIRST_NAME.add("嘉宝");
CN_FIRST_NAME.add("德辉");
CN_FIRST_NAME.add("嘉实");
CN_FIRST_NAME.add("孟阳");
CN_FIRST_NAME.add("瀚玥");
CN_FIRST_NAME.add("安然");
CN_FIRST_NAME.add("昆谊");
CN_FIRST_NAME.add("伶伶");
CN_FIRST_NAME.add("秀梅");
CN_FIRST_NAME.add("曼丽");
CN_FIRST_NAME.add("宏邈");
CN_FIRST_NAME.add("敏才");
CN_FIRST_NAME.add("良策");
CN_FIRST_NAME.add("乐欣");
CN_FIRST_NAME.add("嘉容");
CN_FIRST_NAME.add("琲瓃");
CN_FIRST_NAME.add("半烟");
CN_FIRST_NAME.add("笑翠");
CN_FIRST_NAME.add("莹玉");
CN_FIRST_NAME.add("念桃");
CN_FIRST_NAME.add("英毅");
CN_FIRST_NAME.add("芳华");
CN_FIRST_NAME.add("仙媛");
CN_FIRST_NAME.add("景彰");
CN_FIRST_NAME.add("志诚");
CN_FIRST_NAME.add("素怀");
CN_FIRST_NAME.add("千凝");
CN_FIRST_NAME.add("怀曼");
CN_FIRST_NAME.add("文宣");
CN_FIRST_NAME.add("祺然");
CN_FIRST_NAME.add("千凡");
CN_FIRST_NAME.add("德运");
CN_FIRST_NAME.add("寒梅");
CN_FIRST_NAME.add("斯雅");
CN_FIRST_NAME.add("华灿");
CN_FIRST_NAME.add("承福");
CN_FIRST_NAME.add("音悦");
CN_FIRST_NAME.add("秋蝶");
CN_FIRST_NAME.add("兴言");
CN_FIRST_NAME.add("景龙");
CN_FIRST_NAME.add("骏俊");
CN_FIRST_NAME.add("桂月");
CN_FIRST_NAME.add("春梅");
CN_FIRST_NAME.add("欣跃");
CN_FIRST_NAME.add("平露");
CN_FIRST_NAME.add("曼云");
CN_FIRST_NAME.add("新雅");
CN_FIRST_NAME.add("乐正");
CN_FIRST_NAME.add("梦竹");
CN_FIRST_NAME.add("寒梦");
CN_FIRST_NAME.add("醉蝶");
CN_FIRST_NAME.add("丹丹");
CN_FIRST_NAME.add("高朗");
CN_FIRST_NAME.add("思莹");
CN_FIRST_NAME.add("旭辉");
CN_FIRST_NAME.add("新雨");
CN_FIRST_NAME.add("新雪");
CN_FIRST_NAME.add("雅蕊");
CN_FIRST_NAME.add("忆丹");
CN_FIRST_NAME.add("思莲");
CN_FIRST_NAME.add("阳霁");
CN_FIRST_NAME.add("淳雅");
CN_FIRST_NAME.add("代秋");
CN_FIRST_NAME.add("孤阳");
CN_FIRST_NAME.add("意智");
CN_FIRST_NAME.add("稷骞");
CN_FIRST_NAME.add("寻菡");
CN_FIRST_NAME.add("忆之");
CN_FIRST_NAME.add("卓逸");
CN_FIRST_NAME.add("彩妍");
CN_FIRST_NAME.add("庆生");
CN_FIRST_NAME.add("伶俐");
CN_FIRST_NAME.add("子墨");
CN_FIRST_NAME.add("康伯");
CN_FIRST_NAME.add("绮梅");
CN_FIRST_NAME.add("寻菱");
CN_FIRST_NAME.add("念梦");
CN_FIRST_NAME.add("新霁");
CN_FIRST_NAME.add("苇然");
CN_FIRST_NAME.add("雁易");
CN_FIRST_NAME.add("建木");
CN_FIRST_NAME.add("秋柔");
CN_FIRST_NAME.add("宏儒");
CN_FIRST_NAME.add("光辉");
CN_FIRST_NAME.add("秋柏");
CN_FIRST_NAME.add("半兰");
CN_FIRST_NAME.add("令秋");
CN_FIRST_NAME.add("凯安");
CN_FIRST_NAME.add("丹云");
CN_FIRST_NAME.add("天宇");
CN_FIRST_NAME.add("绮梦");
CN_FIRST_NAME.add("慈心");
CN_FIRST_NAME.add("思菱");
CN_FIRST_NAME.add("海昌");
CN_FIRST_NAME.add("建本");
CN_FIRST_NAME.add("智纯");
CN_FIRST_NAME.add("名姝");
CN_FIRST_NAME.add("莹琇");
CN_FIRST_NAME.add("明诚");
CN_FIRST_NAME.add("凯定");
CN_FIRST_NAME.add("静珊");
CN_FIRST_NAME.add("思萌");
CN_FIRST_NAME.add("丹亦");
CN_FIRST_NAME.add("彭祖");
CN_FIRST_NAME.add("靖琪");
CN_FIRST_NAME.add("秋柳");
CN_FIRST_NAME.add("英豪");
CN_FIRST_NAME.add("幼白");
CN_FIRST_NAME.add("高杰");
CN_FIRST_NAME.add("冬莲");
CN_FIRST_NAME.add("格格");
CN_FIRST_NAME.add("任真");
CN_FIRST_NAME.add("晴美");
CN_FIRST_NAME.add("乐语");
CN_FIRST_NAME.add("丹溪");
CN_FIRST_NAME.add("元灵");
CN_FIRST_NAME.add("醉柳");
CN_FIRST_NAME.add("晓莉");
CN_FIRST_NAME.add("骏逸");
CN_FIRST_NAME.add("若淑");
CN_FIRST_NAME.add("恨竹");
CN_FIRST_NAME.add("凌翠");
CN_FIRST_NAME.add("娟巧");
CN_FIRST_NAME.add("桂枫");
CN_FIRST_NAME.add("萧曼");
CN_FIRST_NAME.add("熙星");
CN_FIRST_NAME.add("锐立");
CN_FIRST_NAME.add("博达");
CN_FIRST_NAME.add("梦安");
CN_FIRST_NAME.add("雅旋");
CN_FIRST_NAME.add("思萱");
CN_FIRST_NAME.add("觅风");
CN_FIRST_NAME.add("光远");
CN_FIRST_NAME.add("白云");
CN_FIRST_NAME.add("初阳");
CN_FIRST_NAME.add("致欣");
CN_FIRST_NAME.add("香之");
CN_FIRST_NAME.add("文山");
CN_FIRST_NAME.add("白亦");
CN_FIRST_NAME.add("微熹");
CN_FIRST_NAME.add("博远");
CN_FIRST_NAME.add("季雅");
CN_FIRST_NAME.add("淳静");
CN_FIRST_NAME.add("漾漾");
CN_FIRST_NAME.add("冬菱");
CN_FIRST_NAME.add("向秋");
CN_FIRST_NAME.add("麦冬");
CN_FIRST_NAME.add("婀娜");
CN_FIRST_NAME.add("怀柔");
CN_FIRST_NAME.add("瀚钰");
CN_FIRST_NAME.add("妙之");
CN_FIRST_NAME.add("宜修");
CN_FIRST_NAME.add("瑞灵");
CN_FIRST_NAME.add("半凡");
CN_FIRST_NAME.add("梦容");
CN_FIRST_NAME.add("梦寒");
CN_FIRST_NAME.add("芷珊");
CN_FIRST_NAME.add("骞仕");
CN_FIRST_NAME.add("芷珍");
CN_FIRST_NAME.add("永贞");
CN_FIRST_NAME.add("乐水");
CN_FIRST_NAME.add("灵槐");
CN_FIRST_NAME.add("婷玉");
CN_FIRST_NAME.add("觅夏");
CN_FIRST_NAME.add("含雁");
CN_FIRST_NAME.add("一嘉");
CN_FIRST_NAME.add("虹彩");
CN_FIRST_NAME.add("韦茹");
CN_FIRST_NAME.add("雅昶");
CN_FIRST_NAME.add("冰莹");
CN_FIRST_NAME.add("悦可");
CN_FIRST_NAME.add("虹影");
CN_FIRST_NAME.add("博瀚");
CN_FIRST_NAME.add("令婧");
CN_FIRST_NAME.add("志泽");
CN_FIRST_NAME.add("冬萱");
CN_FIRST_NAME.add("睿达");
CN_FIRST_NAME.add("伟博");
CN_FIRST_NAME.add("惜海");
CN_FIRST_NAME.add("乐池");
CN_FIRST_NAME.add("幻露");
CN_FIRST_NAME.add("开朗");
CN_FIRST_NAME.add("建柏");
CN_FIRST_NAME.add("方雅");
CN_FIRST_NAME.add("雅晗");
CN_FIRST_NAME.add("奇颖");
CN_FIRST_NAME.add("康适");
CN_FIRST_NAME.add("婉奕");
CN_FIRST_NAME.add("凡巧");
CN_FIRST_NAME.add("幼霜");
CN_FIRST_NAME.add("曼辞");
CN_FIRST_NAME.add("天籁");
CN_FIRST_NAME.add("华采");
CN_FIRST_NAME.add("优瑗");
CN_FIRST_NAME.add("希蓉");
CN_FIRST_NAME.add("新知");
CN_FIRST_NAME.add("皎洁");
CN_FIRST_NAME.add("依萱");
CN_FIRST_NAME.add("夏彤");
CN_FIRST_NAME.add("静和");
CN_FIRST_NAME.add("景胜");
CN_FIRST_NAME.add("芷琪");
CN_FIRST_NAME.add("卓然");
CN_FIRST_NAME.add("和歌");
CN_FIRST_NAME.add("怿悦");
CN_FIRST_NAME.add("冰菱");
CN_FIRST_NAME.add("旭炎");
CN_FIRST_NAME.add("怀桃");
CN_FIRST_NAME.add("端敏");
CN_FIRST_NAME.add("鹏鲲");
CN_FIRST_NAME.add("经赋");
CN_FIRST_NAME.add("瑜然");
CN_FIRST_NAME.add("竹萱");
CN_FIRST_NAME.add("绿蝶");
CN_FIRST_NAME.add("智美");
CN_FIRST_NAME.add("鹏鲸");
CN_FIRST_NAME.add("若云");
CN_FIRST_NAME.add("建树");
CN_FIRST_NAME.add("和正");
CN_FIRST_NAME.add("如冬");
CN_FIRST_NAME.add("南烟");
CN_FIRST_NAME.add("英资");
CN_FIRST_NAME.add("如冰");
CN_FIRST_NAME.add("恨寒");
CN_FIRST_NAME.add("初雪");
CN_FIRST_NAME.add("德元");
CN_FIRST_NAME.add("盼翠");
CN_FIRST_NAME.add("运鹏");
CN_FIRST_NAME.add("蕙芸");
CN_FIRST_NAME.add("学真");
CN_FIRST_NAME.add("心远");
CN_FIRST_NAME.add("高格");
CN_FIRST_NAME.add("谧辰");
CN_FIRST_NAME.add("飞薇");
CN_FIRST_NAME.add("山雁");
CN_FIRST_NAME.add("飞文");
CN_FIRST_NAME.add("运鸿");
CN_FIRST_NAME.add("荷紫");
CN_FIRST_NAME.add("宏爽");
CN_FIRST_NAME.add("康健");
CN_FIRST_NAME.add("梦山");
CN_FIRST_NAME.add("水丹");
CN_FIRST_NAME.add("蕴美");
CN_FIRST_NAME.add("语雪");
CN_FIRST_NAME.add("听露");
CN_FIRST_NAME.add("智志");
CN_FIRST_NAME.add("朋义");
CN_FIRST_NAME.add("如凡");
CN_FIRST_NAME.add("咏歌");
CN_FIRST_NAME.add("骊燕");
CN_FIRST_NAME.add("水之");
CN_FIRST_NAME.add("琪睿");
CN_FIRST_NAME.add("婉秀");
CN_FIRST_NAME.add("云蔚");
CN_FIRST_NAME.add("忆辰");
CN_FIRST_NAME.add("鹤骞");
CN_FIRST_NAME.add("清嘉");
CN_FIRST_NAME.add("冷荷");
CN_FIRST_NAME.add("悦和");
CN_FIRST_NAME.add("怀梦");
CN_FIRST_NAME.add("畅畅");
CN_FIRST_NAME.add("辰良");
CN_FIRST_NAME.add("涵忍");
CN_FIRST_NAME.add("俊弼");
CN_FIRST_NAME.add("梦岚");
CN_FIRST_NAME.add("蕙若");
CN_FIRST_NAME.add("哲彦");
CN_FIRST_NAME.add("绿柏");
CN_FIRST_NAME.add("明洁");
CN_FIRST_NAME.add("初露");
CN_FIRST_NAME.add("皓洁");
CN_FIRST_NAME.add("腾骏");
CN_FIRST_NAME.add("修竹");
CN_FIRST_NAME.add("元冬");
CN_FIRST_NAME.add("凝绿");
CN_FIRST_NAME.add("庄雅");
CN_FIRST_NAME.add("杉月");
CN_FIRST_NAME.add("菊华");
CN_FIRST_NAME.add("哲美");
CN_FIRST_NAME.add("俊彦");
CN_FIRST_NAME.add("米雪");
CN_FIRST_NAME.add("叶帆");
CN_FIRST_NAME.add("忆远");
CN_FIRST_NAME.add("雪艳");
CN_FIRST_NAME.add("绿柳");
CN_FIRST_NAME.add("乐贤");
CN_FIRST_NAME.add("思敏");
CN_FIRST_NAME.add("丽佳");
CN_FIRST_NAME.add("又莲");
CN_FIRST_NAME.add("谷之");
CN_FIRST_NAME.add("一雯");
CN_FIRST_NAME.add("安南");
CN_FIRST_NAME.add("晓蓝");
CN_FIRST_NAME.add("承安");
CN_FIRST_NAME.add("阳飇");
CN_FIRST_NAME.add("新颖");
CN_FIRST_NAME.add("安卉");
CN_FIRST_NAME.add("礼骞");
CN_FIRST_NAME.add("腾骞");
CN_FIRST_NAME.add("永丰");
CN_FIRST_NAME.add("飞昂");
CN_FIRST_NAME.add("婉娜");
CN_FIRST_NAME.add("海融");
CN_FIRST_NAME.add("元凯");
CN_FIRST_NAME.add("承宣");
CN_FIRST_NAME.add("俊美");
CN_FIRST_NAME.add("尔芙");
CN_FIRST_NAME.add("曜瑞");
CN_FIRST_NAME.add("宛儿");
CN_FIRST_NAME.add("冷菱");
CN_FIRST_NAME.add("骞信");
CN_FIRST_NAME.add("宜然");
CN_FIRST_NAME.add("以筠");
CN_FIRST_NAME.add("流丽");
CN_FIRST_NAME.add("纳兰");
CN_FIRST_NAME.add("又菡");
CN_FIRST_NAME.add("飞星");
CN_FIRST_NAME.add("阳飙");
CN_FIRST_NAME.add("芦雪");
CN_FIRST_NAME.add("志专");
CN_FIRST_NAME.add("千叶");
CN_FIRST_NAME.add("鸿彩");
CN_FIRST_NAME.add("力行");
CN_FIRST_NAME.add("向笛");
CN_FIRST_NAME.add("飞虎");
CN_FIRST_NAME.add("经业");
CN_FIRST_NAME.add("濮存");
CN_FIRST_NAME.add("冰蓝");
CN_FIRST_NAME.add("俊德");
CN_FIRST_NAME.add("志业");
CN_FIRST_NAME.add("庆雪");
CN_FIRST_NAME.add("谷云");
CN_FIRST_NAME.add("湉湉");
CN_FIRST_NAME.add("阳夏");
CN_FIRST_NAME.add("骏燕");
CN_FIRST_NAME.add("修筠");
CN_FIRST_NAME.add("琴雪");
CN_FIRST_NAME.add("梓彤");
CN_FIRST_NAME.add("代容");
CN_FIRST_NAME.add("鸿羲");
CN_FIRST_NAME.add("林帆");
CN_FIRST_NAME.add("娅芳");
CN_FIRST_NAME.add("子骞");
CN_FIRST_NAME.add("良工");
CN_FIRST_NAME.add("迎彤");
CN_FIRST_NAME.add("鸿德");
CN_FIRST_NAME.add("鸿羽");
CN_FIRST_NAME.add("冷萱");
CN_FIRST_NAME.add("惠丽");
CN_FIRST_NAME.add("悦畅");
CN_FIRST_NAME.add("熙柔");
CN_FIRST_NAME.add("和豫");
CN_FIRST_NAME.add("经义");
CN_FIRST_NAME.add("梓美");
CN_FIRST_NAME.add("庄静");
CN_FIRST_NAME.add("志义");
CN_FIRST_NAME.add("昊东");
CN_FIRST_NAME.add("丰熙");
CN_FIRST_NAME.add("哲思");
CN_FIRST_NAME.add("忆灵");
CN_FIRST_NAME.add("弘文");
CN_FIRST_NAME.add("慕思");
CN_FIRST_NAME.add("傲菡");
CN_FIRST_NAME.add("安双");
CN_FIRST_NAME.add("夜绿");
CN_FIRST_NAME.add("安珊");
CN_FIRST_NAME.add("鸿志");
CN_FIRST_NAME.add("慧巧");
CN_FIRST_NAME.add("清雅");
CN_FIRST_NAME.add("荏苒");
CN_FIRST_NAME.add("沛芹");
CN_FIRST_NAME.add("光熙");
CN_FIRST_NAME.add("彭魄");
CN_FIRST_NAME.add("昌淼");
CN_FIRST_NAME.add("柔雅");
CN_FIRST_NAME.add("茹薇");
CN_FIRST_NAME.add("依薇");
CN_FIRST_NAME.add("嘉平");
CN_FIRST_NAME.add("嘉年");
CN_FIRST_NAME.add("寻春");
CN_FIRST_NAME.add("以寒");
CN_FIRST_NAME.add("泽雨");
CN_FIRST_NAME.add("暄美");
CN_FIRST_NAME.add("晓蕾");
CN_FIRST_NAME.add("兰泽");
CN_FIRST_NAME.add("友菱");
CN_FIRST_NAME.add("凝心");
CN_FIRST_NAME.add("涵育");
CN_FIRST_NAME.add("荌荌");
CN_FIRST_NAME.add("清霁");
CN_FIRST_NAME.add("陶然");
CN_FIRST_NAME.add("弘新");
CN_FIRST_NAME.add("寄波");
CN_FIRST_NAME.add("俏美");
CN_FIRST_NAME.add("嘉庆");
CN_FIRST_NAME.add("勇捷");
CN_FIRST_NAME.add("红叶");
CN_FIRST_NAME.add("孟夏");
CN_FIRST_NAME.add("子童");
CN_FIRST_NAME.add("宏博");
CN_FIRST_NAME.add("丝琦");
CN_FIRST_NAME.add("海桃");
CN_FIRST_NAME.add("丝琪");
CN_FIRST_NAME.add("经亘");
CN_FIRST_NAME.add("沛若");
CN_FIRST_NAME.add("宛凝");
CN_FIRST_NAME.add("弘方");
CN_FIRST_NAME.add("安吉");
CN_FIRST_NAME.add("之云");
CN_FIRST_NAME.add("雁桃");
CN_FIRST_NAME.add("君婷");
CN_FIRST_NAME.add("锦程");
CN_FIRST_NAME.add("雅柏");
CN_FIRST_NAME.add("昊乾");
CN_FIRST_NAME.add("悦喜");
CN_FIRST_NAME.add("浩言");
CN_FIRST_NAME.add("锐精");
CN_FIRST_NAME.add("雅柔");
CN_FIRST_NAME.add("可心");
CN_FIRST_NAME.add("嘉纳");
CN_FIRST_NAME.add("才艺");
CN_FIRST_NAME.add("芮雅");
CN_FIRST_NAME.add("半双");
CN_FIRST_NAME.add("青雪");
CN_FIRST_NAME.add("安琪");
CN_FIRST_NAME.add("鹏鹍");
CN_FIRST_NAME.add("才良");
CN_FIRST_NAME.add("丹烟");
CN_FIRST_NAME.add("怜晴");
CN_FIRST_NAME.add("晓旋");
CN_FIRST_NAME.add("小萍");
CN_FIRST_NAME.add("天巧");
CN_FIRST_NAME.add("天工");
CN_FIRST_NAME.add("雨莲");
CN_FIRST_NAME.add("冰薇");
CN_FIRST_NAME.add("晗蕊");
CN_FIRST_NAME.add("孤风");
CN_FIRST_NAME.add("乐游");
CN_FIRST_NAME.add("元勋");
CN_FIRST_NAME.add("洁雅");
CN_FIRST_NAME.add("阳秋");
CN_FIRST_NAME.add("凝思");
CN_FIRST_NAME.add("冬易");
CN_FIRST_NAME.add("和泰");
CN_FIRST_NAME.add("莹白");
CN_FIRST_NAME.add("良平");
CN_FIRST_NAME.add("雁梅");
CN_FIRST_NAME.add("涵意");
CN_FIRST_NAME.add("和泽");
CN_FIRST_NAME.add("慕悦");
CN_FIRST_NAME.add("乐湛");
CN_FIRST_NAME.add("幻天");
CN_FIRST_NAME.add("星汉");
CN_FIRST_NAME.add("柔静");
CN_FIRST_NAME.add("朗丽");
CN_FIRST_NAME.add("晗蕾");
CN_FIRST_NAME.add("奥雅");
CN_FIRST_NAME.add("雪莲");
CN_FIRST_NAME.add("文康");
CN_FIRST_NAME.add("如南");
CN_FIRST_NAME.add("又蓝");
CN_FIRST_NAME.add("俊悟");
CN_FIRST_NAME.add("佁然");
CN_FIRST_NAME.add("若灵");
CN_FIRST_NAME.add("晓星");
CN_FIRST_NAME.add("长运");
CN_FIRST_NAME.add("叶彤");
CN_FIRST_NAME.add("安和");
CN_FIRST_NAME.add("悠雅");
CN_FIRST_NAME.add("祺瑞");
CN_FIRST_NAME.add("晓昕");
CN_FIRST_NAME.add("驰皓");
CN_FIRST_NAME.add("琴音");
CN_FIRST_NAME.add("翠丝");
CN_FIRST_NAME.add("子安");
CN_FIRST_NAME.add("元化");
CN_FIRST_NAME.add("兴贤");
CN_FIRST_NAME.add("子宁");
CN_FIRST_NAME.add("和洽");
CN_FIRST_NAME.add("曼冬");
CN_FIRST_NAME.add("忆然");
CN_FIRST_NAME.add("平婉");
CN_FIRST_NAME.add("子实");
CN_FIRST_NAME.add("启颜");
CN_FIRST_NAME.add("多思");
CN_FIRST_NAME.add("才英");
CN_FIRST_NAME.add("书语");
CN_FIRST_NAME.add("琴韵");
CN_FIRST_NAME.add("绍辉");
CN_FIRST_NAME.add("静白");
CN_FIRST_NAME.add("昊伟");
CN_FIRST_NAME.add("齐心");
CN_FIRST_NAME.add("立诚");
CN_FIRST_NAME.add("月灵");
CN_FIRST_NAME.add("依晨");
CN_FIRST_NAME.add("天干");
CN_FIRST_NAME.add("晗日");
CN_FIRST_NAME.add("乐人");
CN_FIRST_NAME.add("坚白");
CN_FIRST_NAME.add("曼凡");
CN_FIRST_NAME.add("驰雪");
CN_FIRST_NAME.add("明亮");
CN_FIRST_NAME.add("曼凝");
CN_FIRST_NAME.add("玉泉");
CN_FIRST_NAME.add("信鸥");
CN_FIRST_NAME.add("雪萍");
CN_FIRST_NAME.add("幻香");
CN_FIRST_NAME.add("飞松");
CN_FIRST_NAME.add("信鸿");
CN_FIRST_NAME.add("洁静");
CN_FIRST_NAME.add("希月");
CN_FIRST_NAME.add("诗筠");
CN_FIRST_NAME.add("星河");
CN_FIRST_NAME.add("罗绮");
CN_FIRST_NAME.add("问芙");
CN_FIRST_NAME.add("俊能");
CN_FIRST_NAME.add("芮静");
CN_FIRST_NAME.add("德华");
CN_FIRST_NAME.add("欣然");
CN_FIRST_NAME.add("翰池");
CN_FIRST_NAME.add("晨菲");
CN_FIRST_NAME.add("向山");
CN_FIRST_NAME.add("长逸");
CN_FIRST_NAME.add("忻欢");
CN_FIRST_NAME.add("晔晔");
CN_FIRST_NAME.add("语风");
CN_FIRST_NAME.add("运恒");
CN_FIRST_NAME.add("佑运");
CN_FIRST_NAME.add("初夏");
CN_FIRST_NAME.add("玉泽");
CN_FIRST_NAME.add("婉容");
CN_FIRST_NAME.add("清韵");
CN_FIRST_NAME.add("静雅");
CN_FIRST_NAME.add("凯康");
CN_FIRST_NAME.add("飞柏");
CN_FIRST_NAME.add("天纵");
CN_FIRST_NAME.add("奕奕");
CN_FIRST_NAME.add("嘉美");
CN_FIRST_NAME.add("星波");
CN_FIRST_NAME.add("星泽");
CN_FIRST_NAME.add("文彦");
CN_FIRST_NAME.add("颐然");
CN_FIRST_NAME.add("晗昱");
CN_FIRST_NAME.add("苑博");
CN_FIRST_NAME.add("良弼");
CN_FIRST_NAME.add("曦哲");
CN_FIRST_NAME.add("梅花");
CN_FIRST_NAME.add("含香");
CN_FIRST_NAME.add("嘉德");
CN_FIRST_NAME.add("晨萱");
CN_FIRST_NAME.add("才捷");
CN_FIRST_NAME.add("德厚");
CN_FIRST_NAME.add("文彬");
CN_FIRST_NAME.add("布衣");
CN_FIRST_NAME.add("炫明");
CN_FIRST_NAME.add("映波");
CN_FIRST_NAME.add("力言");
CN_FIRST_NAME.add("易云");
CN_FIRST_NAME.add("作人");
CN_FIRST_NAME.add("俊慧");
CN_FIRST_NAME.add("采莲");
CN_FIRST_NAME.add("沛萍");
CN_FIRST_NAME.add("嘉志");
CN_FIRST_NAME.add("燕舞");
CN_FIRST_NAME.add("葛菲");
CN_FIRST_NAME.add("星津");
CN_FIRST_NAME.add("晗晗");
CN_FIRST_NAME.add("卿云");
CN_FIRST_NAME.add("英达");
CN_FIRST_NAME.add("含秀");
CN_FIRST_NAME.add("星洲");
CN_FIRST_NAME.add("梅英");
CN_FIRST_NAME.add("灵波");
CN_FIRST_NAME.add("芷雪");
CN_FIRST_NAME.add("晓曼");
CN_FIRST_NAME.add("敏智");
CN_FIRST_NAME.add("白凡");
CN_FIRST_NAME.add("怡月");
CN_FIRST_NAME.add("慧美");
CN_FIRST_NAME.add("思松");
CN_FIRST_NAME.add("永逸");
CN_FIRST_NAME.add("白凝");
CN_FIRST_NAME.add("浩歌");
CN_FIRST_NAME.add("玄清");
CN_FIRST_NAME.add("文心");
CN_FIRST_NAME.add("小蕊");
CN_FIRST_NAME.add("盼芙");
CN_FIRST_NAME.add("笑萍");
CN_FIRST_NAME.add("惜灵");
CN_FIRST_NAME.add("明轩");
CN_FIRST_NAME.add("新立");
CN_FIRST_NAME.add("吉帆");
CN_FIRST_NAME.add("流逸");
CN_FIRST_NAME.add("文德");
CN_FIRST_NAME.add("傲薇");
CN_FIRST_NAME.add("会雯");
CN_FIRST_NAME.add("竹月");
CN_FIRST_NAME.add("思枫");
CN_FIRST_NAME.add("卓君");
CN_FIRST_NAME.add("雅楠");
CN_FIRST_NAME.add("怡木");
CN_FIRST_NAME.add("兴业");
CN_FIRST_NAME.add("光华");
CN_FIRST_NAME.add("慧心");
CN_FIRST_NAME.add("双文");
CN_FIRST_NAME.add("嘉怡");
CN_FIRST_NAME.add("湘云");
CN_FIRST_NAME.add("星海");
CN_FIRST_NAME.add("含娇");
CN_FIRST_NAME.add("明辉");
CN_FIRST_NAME.add("皓轩");
CN_FIRST_NAME.add("琼音");
CN_FIRST_NAME.add("若兰");
CN_FIRST_NAME.add("瑛琭");
CN_FIRST_NAME.add("尔蓉");
CN_FIRST_NAME.add("尔蓝");
CN_FIRST_NAME.add("小蕾");
CN_FIRST_NAME.add("文翰");
CN_FIRST_NAME.add("新竹");
CN_FIRST_NAME.add("寄云");
CN_FIRST_NAME.add("兴为");
CN_FIRST_NAME.add("楚楚");
CN_FIRST_NAME.add("秀洁");
CN_FIRST_NAME.add("傲旋");
CN_FIRST_NAME.add("天罡");
CN_FIRST_NAME.add("文耀");
CN_FIRST_NAME.add("采萱");
CN_FIRST_NAME.add("思柔");
CN_FIRST_NAME.add("南珍");
CN_FIRST_NAME.add("觅山");
CN_FIRST_NAME.add("温瑜");
CN_FIRST_NAME.add("平宁");
CN_FIRST_NAME.add("晨蓓");
CN_FIRST_NAME.add("高歌");
CN_FIRST_NAME.add("莺韵");
CN_FIRST_NAME.add("代巧");
CN_FIRST_NAME.add("明俊");
CN_FIRST_NAME.add("良翰");
CN_FIRST_NAME.add("颖然");
CN_FIRST_NAME.add("瑛瑶");
CN_FIRST_NAME.add("英逸");
CN_FIRST_NAME.add("昂然");
CN_FIRST_NAME.add("文思");
CN_FIRST_NAME.add("胤运");
CN_FIRST_NAME.add("明达");
CN_FIRST_NAME.add("平安");
CN_FIRST_NAME.add("溪蓝");
CN_FIRST_NAME.add("骏琛");
CN_FIRST_NAME.add("明远");
CN_FIRST_NAME.add("霞绮");
CN_FIRST_NAME.add("馨逸");
CN_FIRST_NAME.add("水儿");
CN_FIRST_NAME.add("梦影");
CN_FIRST_NAME.add("翰海");
CN_FIRST_NAME.add("虹英");
CN_FIRST_NAME.add("博厚");
CN_FIRST_NAME.add("雨文");
CN_FIRST_NAME.add("晶茹");
CN_FIRST_NAME.add("访彤");
CN_FIRST_NAME.add("筠竹");
CN_FIRST_NAME.add("元瑶");
CN_FIRST_NAME.add("宏畅");
CN_FIRST_NAME.add("鹏翼");
CN_FIRST_NAME.add("友易");
CN_FIRST_NAME.add("寻桃");
CN_FIRST_NAME.add("又晴");
CN_FIRST_NAME.add("傲易");
CN_FIRST_NAME.add("沛蓝");
CN_FIRST_NAME.add("芸静");
CN_FIRST_NAME.add("天心");
CN_FIRST_NAME.add("晓枫");
CN_FIRST_NAME.add("睿博");
CN_FIRST_NAME.add("一禾");
CN_FIRST_NAME.add("嘉悦");
CN_FIRST_NAME.add("南琴");
CN_FIRST_NAME.add("绮波");
CN_FIRST_NAME.add("美如");
CN_FIRST_NAME.add("新筠");
CN_FIRST_NAME.add("安阳");
CN_FIRST_NAME.add("曼卉");
CN_FIRST_NAME.add("霁芸");
CN_FIRST_NAME.add("朋兴");
CN_FIRST_NAME.add("秀越");
CN_FIRST_NAME.add("浩气");
CN_FIRST_NAME.add("星渊");
CN_FIRST_NAME.add("长兴");
CN_FIRST_NAME.add("俊才");
CN_FIRST_NAME.add("冰蝶");
CN_FIRST_NAME.add("问萍");
CN_FIRST_NAME.add("瑜璟");
CN_FIRST_NAME.add("典丽");
CN_FIRST_NAME.add("梓舒");
CN_FIRST_NAME.add("千雁");
CN_FIRST_NAME.add("幻竹");
CN_FIRST_NAME.add("承平");
CN_FIRST_NAME.add("昂熙");
CN_FIRST_NAME.add("依柔");
CN_FIRST_NAME.add("韦曲");
CN_FIRST_NAME.add("恬默");
CN_FIRST_NAME.add("寻梅");
CN_FIRST_NAME.add("乐逸");
CN_FIRST_NAME.add("采蓝");
CN_FIRST_NAME.add("亦旋");
CN_FIRST_NAME.add("天翰");
CN_FIRST_NAME.add("清奇");
CN_FIRST_NAME.add("俊良");
CN_FIRST_NAME.add("惜儿");
CN_FIRST_NAME.add("彦红");
CN_FIRST_NAME.add("雨旋");
CN_FIRST_NAME.add("冰枫");
CN_FIRST_NAME.add("玉书");
CN_FIRST_NAME.add("水冬");
CN_FIRST_NAME.add("嘉胜");
CN_FIRST_NAME.add("小星");
CN_FIRST_NAME.add("嘉惠");
CN_FIRST_NAME.add("小春");
CN_FIRST_NAME.add("鸿才");
CN_FIRST_NAME.add("俊艾");
CN_FIRST_NAME.add("春海");
CN_FIRST_NAME.add("菱凡");
CN_FIRST_NAME.add("霞影");
CN_FIRST_NAME.add("曜坤");
CN_FIRST_NAME.add("永元");
CN_FIRST_NAME.add("傲晴");
CN_FIRST_NAME.add("谷兰");
CN_FIRST_NAME.add("韶敏");
CN_FIRST_NAME.add("光启");
CN_FIRST_NAME.add("楠楠");
CN_FIRST_NAME.add("绍元");
CN_FIRST_NAME.add("安白");
CN_FIRST_NAME.add("水凡");
CN_FIRST_NAME.add("高谊");
CN_FIRST_NAME.add("清妍");
CN_FIRST_NAME.add("雨星");
CN_FIRST_NAME.add("莞尔");
CN_FIRST_NAME.add("紫菱");
CN_FIRST_NAME.add("骞北");
CN_FIRST_NAME.add("小晨");
CN_FIRST_NAME.add("文惠");
CN_FIRST_NAME.add("蓉城");
CN_FIRST_NAME.add("驰颖");
CN_FIRST_NAME.add("丹南");
CN_FIRST_NAME.add("清妙");
CN_FIRST_NAME.add("云梦");
CN_FIRST_NAME.add("俊拔");
CN_FIRST_NAME.add("沛文");
CN_FIRST_NAME.add("元甲");
CN_FIRST_NAME.add("柔妙");
CN_FIRST_NAME.add("紫萍");
CN_FIRST_NAME.add("清馨");
CN_FIRST_NAME.add("修平");
CN_FIRST_NAME.add("骏哲");
CN_FIRST_NAME.add("理群");
CN_FIRST_NAME.add("晓桐");
CN_FIRST_NAME.add("冬梅");
CN_FIRST_NAME.add("波峻");
CN_FIRST_NAME.add("颖初");
CN_FIRST_NAME.add("凝芙");
CN_FIRST_NAME.add("忆南");
CN_FIRST_NAME.add("浦泽");
CN_FIRST_NAME.add("惠然");
CN_FIRST_NAME.add("哲茂");
CN_FIRST_NAME.add("远悦");
CN_FIRST_NAME.add("乐邦");
CN_FIRST_NAME.add("曼珍");
CN_FIRST_NAME.add("昊然");
CN_FIRST_NAME.add("丝雨");
CN_FIRST_NAME.add("白卉");
CN_FIRST_NAME.add("嘉慕");
CN_FIRST_NAME.add("曼珠");
CN_FIRST_NAME.add("英光");
CN_FIRST_NAME.add("紫萱");
CN_FIRST_NAME.add("芬馥");
CN_FIRST_NAME.add("清秋");
CN_FIRST_NAME.add("天恩");
CN_FIRST_NAME.add("醉波");
CN_FIRST_NAME.add("昊焱");
CN_FIRST_NAME.add("俊英");
CN_FIRST_NAME.add("宏阔");
CN_FIRST_NAME.add("秀丽");
CN_FIRST_NAME.add("俊茂");
CN_FIRST_NAME.add("致远");
CN_FIRST_NAME.add("幼安");
CN_FIRST_NAME.add("瑞锦");
CN_FIRST_NAME.add("红雪");
CN_FIRST_NAME.add("晨旭");
CN_FIRST_NAME.add("彤彤");
CN_FIRST_NAME.add("合美");
CN_FIRST_NAME.add("运良");
CN_FIRST_NAME.add("展鹏");
CN_FIRST_NAME.add("承弼");
CN_FIRST_NAME.add("雨晨");
CN_FIRST_NAME.add("浩波");
CN_FIRST_NAME.add("妍和");
CN_FIRST_NAME.add("青香");
CN_FIRST_NAME.add("世韵");
CN_FIRST_NAME.add("天悦");
CN_FIRST_NAME.add("芝宇");
CN_FIRST_NAME.add("泰宁");
CN_FIRST_NAME.add("雨晴");
CN_FIRST_NAME.add("安国");
CN_FIRST_NAME.add("飞槐");
CN_FIRST_NAME.add("碧灵");
CN_FIRST_NAME.add("白玉");
CN_FIRST_NAME.add("坚壁");
CN_FIRST_NAME.add("冷松");
CN_FIRST_NAME.add("恬美");
CN_FIRST_NAME.add("曼吟");
CN_FIRST_NAME.add("采薇");
CN_FIRST_NAME.add("采文");
CN_FIRST_NAME.add("鸣晨");
CN_FIRST_NAME.add("丽华");
CN_FIRST_NAME.add("夏菡");
CN_FIRST_NAME.add("悠奕");
CN_FIRST_NAME.add("晨星");
CN_FIRST_NAME.add("智菱");
CN_FIRST_NAME.add("韦柔");
CN_FIRST_NAME.add("又松");
CN_FIRST_NAME.add("子帆");
CN_FIRST_NAME.add("听筠");
CN_FIRST_NAME.add("涵菡");
CN_FIRST_NAME.add("香卉");
CN_FIRST_NAME.add("安露");
CN_FIRST_NAME.add("鸿振");
CN_FIRST_NAME.add("骏喆");
CN_FIRST_NAME.add("歌云");
CN_FIRST_NAME.add("音景");
CN_FIRST_NAME.add("涵菱");
CN_FIRST_NAME.add("童欣");
CN_FIRST_NAME.add("笑旋");
CN_FIRST_NAME.add("锐志");
CN_FIRST_NAME.add("开诚");
CN_FIRST_NAME.add("兴运");
CN_FIRST_NAME.add("听安");
CN_FIRST_NAME.add("雪晴");
CN_FIRST_NAME.add("馨兰");
CN_FIRST_NAME.add("正诚");
CN_FIRST_NAME.add("灵溪");
CN_FIRST_NAME.add("桐欣");
CN_FIRST_NAME.add("孤容");
CN_FIRST_NAME.add("曾琪");
CN_FIRST_NAME.add("书云");
CN_FIRST_NAME.add("安青");
CN_FIRST_NAME.add("叶舞");
CN_FIRST_NAME.add("丽玉");
CN_FIRST_NAME.add("乐儿");
CN_FIRST_NAME.add("沛春");
CN_FIRST_NAME.add("三姗");
CN_FIRST_NAME.add("俊捷");
CN_FIRST_NAME.add("清婉");
CN_FIRST_NAME.add("半雪");
CN_FIRST_NAME.add("乐然");
CN_FIRST_NAME.add("思楠");
CN_FIRST_NAME.add("兴修");
CN_FIRST_NAME.add("锐翰");
CN_FIRST_NAME.add("朗然");
CN_FIRST_NAME.add("寒云");
CN_FIRST_NAME.add("柔婉");
CN_FIRST_NAME.add("素昕");
CN_FIRST_NAME.add("安静");
CN_FIRST_NAME.add("念之");
CN_FIRST_NAME.add("绮丽");
CN_FIRST_NAME.add("宛畅");
CN_FIRST_NAME.add("嘉致");
CN_FIRST_NAME.add("巍然");
CN_FIRST_NAME.add("若南");
CN_FIRST_NAME.add("悠馨");
CN_FIRST_NAME.add("和通");
CN_FIRST_NAME.add("又柔");
CN_FIRST_NAME.add("傲松");
CN_FIRST_NAME.add("夏萱");
CN_FIRST_NAME.add("正谊");
CN_FIRST_NAME.add("问蕊");
CN_FIRST_NAME.add("玉轩");
CN_FIRST_NAME.add("华皓");
CN_FIRST_NAME.add("湘灵");
CN_FIRST_NAME.add("丹琴");
CN_FIRST_NAME.add("明煦");
CN_FIRST_NAME.add("承德");
CN_FIRST_NAME.add("以彤");
CN_FIRST_NAME.add("若华");
CN_FIRST_NAME.add("嘉懿");
CN_FIRST_NAME.add("锐思");
CN_FIRST_NAME.add("令美");
CN_FIRST_NAME.add("欣可");
CN_FIRST_NAME.add("淑惠");
CN_FIRST_NAME.add("宏盛");
CN_FIRST_NAME.add("子平");
CN_FIRST_NAME.add("修齐");
CN_FIRST_NAME.add("元嘉");
CN_FIRST_NAME.add("采春");
CN_FIRST_NAME.add("浩浩");
CN_FIRST_NAME.add("凝荷");
CN_FIRST_NAME.add("浩涆");
CN_FIRST_NAME.add("瑰玮");
CN_FIRST_NAME.add("凌文");
CN_FIRST_NAME.add("成济");
CN_FIRST_NAME.add("承志");
CN_FIRST_NAME.add("雅歌");
CN_FIRST_NAME.add("念云");
CN_FIRST_NAME.add("高洁");
CN_FIRST_NAME.add("寄灵");
CN_FIRST_NAME.add("立人");
CN_FIRST_NAME.add("雪曼");
CN_FIRST_NAME.add("芳馥");
CN_FIRST_NAME.add("芷天");
CN_FIRST_NAME.add("半青");
CN_FIRST_NAME.add("芳馨");
CN_FIRST_NAME.add("懿轩");
CN_FIRST_NAME.add("明熙");
CN_FIRST_NAME.add("欣合");
CN_FIRST_NAME.add("丽珠");
CN_FIRST_NAME.add("月华");
CN_FIRST_NAME.add("问薇");
CN_FIRST_NAME.add("书仪");
CN_FIRST_NAME.add("昌燎");
CN_FIRST_NAME.add("令羽");
CN_FIRST_NAME.add("萌运");
CN_FIRST_NAME.add("天慧");
CN_FIRST_NAME.add("傲柏");
CN_FIRST_NAME.add("妙双");
CN_FIRST_NAME.add("睿哲");
CN_FIRST_NAME.add("妙珍");
CN_FIRST_NAME.add("晓楠");
CN_FIRST_NAME.add("文成");
CN_FIRST_NAME.add("傲柔");
CN_FIRST_NAME.add("依楠");
CN_FIRST_NAME.add("修美");
CN_FIRST_NAME.add("正豪");
CN_FIRST_NAME.add("绮云");
CN_FIRST_NAME.add("菱华");
CN_FIRST_NAME.add("晨曦");
CN_FIRST_NAME.add("景明");
CN_FIRST_NAME.add("丽君");
CN_FIRST_NAME.add("小枫");
CN_FIRST_NAME.add("叶芳");
CN_FIRST_NAME.add("迎荷");
CN_FIRST_NAME.add("向彤");
CN_FIRST_NAME.add("星辰");
CN_FIRST_NAME.add("凝莲");
CN_FIRST_NAME.add("紫蕙");
CN_FIRST_NAME.add("巧云");
CN_FIRST_NAME.add("明凝");
CN_FIRST_NAME.add("子默");
CN_FIRST_NAME.add("修德");
CN_FIRST_NAME.add("杨柳");
CN_FIRST_NAME.add("布欣");
CN_FIRST_NAME.add("彬彬");
CN_FIRST_NAME.add("梓莹");
CN_FIRST_NAME.add("嘉良");
CN_FIRST_NAME.add("笑晴");
CN_FIRST_NAME.add("波鸿");
CN_FIRST_NAME.add("元白");
CN_FIRST_NAME.add("夏蓉");
CN_FIRST_NAME.add("静秀");
CN_FIRST_NAME.add("轶丽");
CN_FIRST_NAME.add("水卉");
CN_FIRST_NAME.add("翊君");
CN_FIRST_NAME.add("逸雅");
CN_FIRST_NAME.add("雅诗");
CN_FIRST_NAME.add("涵蓄");
CN_FIRST_NAME.add("晨朗");
CN_FIRST_NAME.add("如雪");
CN_FIRST_NAME.add("坚秉");
CN_FIRST_NAME.add("冷梅");
CN_FIRST_NAME.add("悠婉");
CN_FIRST_NAME.add("彭彭");
CN_FIRST_NAME.add("奇希");
CN_FIRST_NAME.add("良才");
CN_FIRST_NAME.add("梓菱");
CN_FIRST_NAME.add("紫文");
CN_FIRST_NAME.add("紫薇");
CN_FIRST_NAME.add("骊雪");
CN_FIRST_NAME.add("令怡");
CN_FIRST_NAME.add("静姝");
CN_FIRST_NAME.add("恬悦");
CN_FIRST_NAME.add("兴邦");
CN_FIRST_NAME.add("暄莹");
CN_FIRST_NAME.add("奥婷");
CN_FIRST_NAME.add("淑慧");
CN_FIRST_NAME.add("忻乐");
CN_FIRST_NAME.add("浩淼");
CN_FIRST_NAME.add("高超");
CN_FIRST_NAME.add("岚霏");
CN_FIRST_NAME.add("承恩");
CN_FIRST_NAME.add("雪松");
CN_FIRST_NAME.add("骊霞");
CN_FIRST_NAME.add("友桃");
CN_FIRST_NAME.add("凌春");
CN_FIRST_NAME.add("箫吟");
CN_FIRST_NAME.add("志勇");
CN_FIRST_NAME.add("远航");
CN_FIRST_NAME.add("慧艳");
CN_FIRST_NAME.add("芸馨");
CN_FIRST_NAME.add("千风");
CN_FIRST_NAME.add("问春");
CN_FIRST_NAME.add("宜嘉");
CN_FIRST_NAME.add("静娴");
CN_FIRST_NAME.add("尔蝶");
CN_FIRST_NAME.add("贞静");
CN_FIRST_NAME.add("英勋");
CN_FIRST_NAME.add("锐意");
CN_FIRST_NAME.add("颐和");
CN_FIRST_NAME.add("运莱");
CN_FIRST_NAME.add("立轩");
CN_FIRST_NAME.add("长卿");
CN_FIRST_NAME.add("梓萱");
CN_FIRST_NAME.add("雨柏");
CN_FIRST_NAME.add("隽洁");
CN_FIRST_NAME.add("饮香");
CN_FIRST_NAME.add("浩丽");
CN_FIRST_NAME.add("浩渺");
CN_FIRST_NAME.add("静婉");
CN_FIRST_NAME.add("成业");
CN_FIRST_NAME.add("承悦");
CN_FIRST_NAME.add("玛丽");
CN_FIRST_NAME.add("天成");
CN_FIRST_NAME.add("凌晓");
CN_FIRST_NAME.add("昆卉");
CN_FIRST_NAME.add("友梅");
CN_FIRST_NAME.add("清宁");
CN_FIRST_NAME.add("立辉");
CN_FIRST_NAME.add("雪枫");
CN_FIRST_NAME.add("嘉茂");
CN_FIRST_NAME.add("驰婷");
CN_FIRST_NAME.add("智敏");
CN_FIRST_NAME.add("阳州");
CN_FIRST_NAME.add("安顺");
CN_FIRST_NAME.add("星火");
CN_FIRST_NAME.add("惜玉");
CN_FIRST_NAME.add("婷秀");
CN_FIRST_NAME.add("凌晴");
CN_FIRST_NAME.add("谷玉");
CN_FIRST_NAME.add("泽宇");
CN_FIRST_NAME.add("运菱");
CN_FIRST_NAME.add("珠星");
CN_FIRST_NAME.add("伟祺");
CN_FIRST_NAME.add("聪慧");
CN_FIRST_NAME.add("昌勋");
CN_FIRST_NAME.add("子美");
CN_FIRST_NAME.add("芸姝");
CN_FIRST_NAME.add("语山");
CN_FIRST_NAME.add("和光");
CN_FIRST_NAME.add("驰媛");
CN_FIRST_NAME.add("景曜");
CN_FIRST_NAME.add("盼旋");
CN_FIRST_NAME.add("婵娟");
CN_FIRST_NAME.add("淑懿");
CN_FIRST_NAME.add("开济");
CN_FIRST_NAME.add("紫易");
CN_FIRST_NAME.add("宛白");
CN_FIRST_NAME.add("偲偲");
CN_FIRST_NAME.add("和煦");
CN_FIRST_NAME.add("尔柳");
CN_FIRST_NAME.add("绿海");
CN_FIRST_NAME.add("之卉");
CN_FIRST_NAME.add("痴旋");
CN_FIRST_NAME.add("雪柳");
CN_FIRST_NAME.add("高义");
CN_FIRST_NAME.add("惜珊");
CN_FIRST_NAME.add("涵蕾");
CN_FIRST_NAME.add("元青");
CN_FIRST_NAME.add("慧英");
CN_FIRST_NAME.add("正浩");
CN_FIRST_NAME.add("建业");
CN_FIRST_NAME.add("英华");
CN_FIRST_NAME.add("嘉荣");
CN_FIRST_NAME.add("中震");
CN_FIRST_NAME.add("玟丽");
CN_FIRST_NAME.add("高丽");
CN_FIRST_NAME.add("秀逸");
CN_FIRST_NAME.add("建中");
CN_FIRST_NAME.add("文茵");
CN_FIRST_NAME.add("建义");
CN_FIRST_NAME.add("贞韵");
CN_FIRST_NAME.add("晴虹");
CN_FIRST_NAME.add("英卫");
CN_FIRST_NAME.add("芮安");
CN_FIRST_NAME.add("雨梅");
CN_FIRST_NAME.add("欣畅");
CN_FIRST_NAME.add("琦巧");
CN_FIRST_NAME.add("英卓");
CN_FIRST_NAME.add("沛柔");
CN_FIRST_NAME.add("亦梅");
CN_FIRST_NAME.add("夏旋");
CN_FIRST_NAME.add("之玉");
CN_FIRST_NAME.add("盼易");
CN_FIRST_NAME.add("慕蕊");
CN_FIRST_NAME.add("英博");
CN_FIRST_NAME.add("丰雅");
CN_FIRST_NAME.add("博雅");
CN_FIRST_NAME.add("茂典");
CN_FIRST_NAME.add("斯年");
CN_FIRST_NAME.add("曲静");
CN_FIRST_NAME.add("觅翠");
CN_FIRST_NAME.add("迎蓉");
CN_FIRST_NAME.add("梓蓓");
CN_FIRST_NAME.add("宏硕");
CN_FIRST_NAME.add("南霜");
CN_FIRST_NAME.add("舒云");
CN_FIRST_NAME.add("艳芳");
CN_FIRST_NAME.add("南露");
CN_FIRST_NAME.add("阳平");
CN_FIRST_NAME.add("悦媛");
CN_FIRST_NAME.add("子怀");
CN_FIRST_NAME.add("歆然");
CN_FIRST_NAME.add("成仁");
CN_FIRST_NAME.add("倩秀");
CN_FIRST_NAME.add("痴春");
CN_FIRST_NAME.add("蕴藉");
CN_FIRST_NAME.add("修能");
CN_FIRST_NAME.add("瑶瑾");
CN_FIRST_NAME.add("幻巧");
CN_FIRST_NAME.add("彦慧");
CN_FIRST_NAME.add("晶晶");
CN_FIRST_NAME.add("雅洁");
CN_FIRST_NAME.add("水瑶");
CN_FIRST_NAME.add("温韦");
CN_FIRST_NAME.add("光霁");
CN_FIRST_NAME.add("青寒");
CN_FIRST_NAME.add("静竹");
CN_FIRST_NAME.add("妍雅");
CN_FIRST_NAME.add("采枫");
CN_FIRST_NAME.add("虹星");
CN_FIRST_NAME.add("智明");
CN_FIRST_NAME.add("从菡");
CN_FIRST_NAME.add("子怡");
CN_FIRST_NAME.add("飞语");
CN_FIRST_NAME.add("甜恬");
CN_FIRST_NAME.add("千秋");
CN_FIRST_NAME.add("海超");
CN_FIRST_NAME.add("平绿");
CN_FIRST_NAME.add("之双");
CN_FIRST_NAME.add("楚洁");
CN_FIRST_NAME.add("婷婷");
CN_FIRST_NAME.add("昆琦");
CN_FIRST_NAME.add("浩漫");
CN_FIRST_NAME.add("涵易");
CN_FIRST_NAME.add("丝祺");
CN_FIRST_NAME.add("敬曦");
CN_FIRST_NAME.add("盼晴");
CN_FIRST_NAME.add("诗翠");
CN_FIRST_NAME.add("星然");
CN_FIRST_NAME.add("慧捷");
CN_FIRST_NAME.add("晴曦");
CN_FIRST_NAME.add("英叡");
CN_FIRST_NAME.add("又槐");
CN_FIRST_NAME.add("长钰");
CN_FIRST_NAME.add("涵映");
CN_FIRST_NAME.add("星光");
CN_FIRST_NAME.add("凝蕊");
CN_FIRST_NAME.add("铭晨");
CN_FIRST_NAME.add("玉兰");
CN_FIRST_NAME.add("令慧");
CN_FIRST_NAME.add("星儿");
CN_FIRST_NAME.add("笑柳");
CN_FIRST_NAME.add("安祯");
CN_FIRST_NAME.add("康盛");
CN_FIRST_NAME.add("正清");
CN_FIRST_NAME.add("智晖");
CN_FIRST_NAME.add("英发");
CN_FIRST_NAME.add("梓敏");
CN_FIRST_NAME.add("含巧");
CN_FIRST_NAME.add("诗怀");
CN_FIRST_NAME.add("正业");
CN_FIRST_NAME.add("元基");
CN_FIRST_NAME.add("采柳");
CN_FIRST_NAME.add("凌蝶");
CN_FIRST_NAME.add("韵梅");
CN_FIRST_NAME.add("祺祥");
CN_FIRST_NAME.add("夜蓉");
CN_FIRST_NAME.add("喜儿");
CN_FIRST_NAME.add("安福");
CN_FIRST_NAME.add("佩兰");
CN_FIRST_NAME.add("自珍");
CN_FIRST_NAME.add("宏壮");
CN_FIRST_NAME.add("惠君");
CN_FIRST_NAME.add("红香");
CN_FIRST_NAME.add("小楠");
CN_FIRST_NAME.add("鸿文");
CN_FIRST_NAME.add("康震");
CN_FIRST_NAME.add("燕晨");
CN_FIRST_NAME.add("静安");
CN_FIRST_NAME.add("泰鸿");
CN_FIRST_NAME.add("耘豪");
CN_FIRST_NAME.add("木兰");
CN_FIRST_NAME.add("寒烟");
CN_FIRST_NAME.add("松月");
CN_FIRST_NAME.add("曼雁");
CN_FIRST_NAME.add("欣嘉");
CN_FIRST_NAME.add("蔚然");
CN_FIRST_NAME.add("安妮");
CN_FIRST_NAME.add("维运");
CN_FIRST_NAME.add("祺福");
CN_FIRST_NAME.add("平彤");
CN_FIRST_NAME.add("子悦");
CN_FIRST_NAME.add("骊颖");
CN_FIRST_NAME.add("迎蕾");
CN_FIRST_NAME.add("凯捷");
CN_FIRST_NAME.add("雁丝");
CN_FIRST_NAME.add("友槐");
CN_FIRST_NAME.add("问枫");
CN_FIRST_NAME.add("紫杉");
CN_FIRST_NAME.add("宏大");
CN_FIRST_NAME.add("乐珍");
CN_FIRST_NAME.add("乐双");
CN_FIRST_NAME.add("绍钧");
CN_FIRST_NAME.add("飞沉");
CN_FIRST_NAME.add("奇志");
CN_FIRST_NAME.add("思语");
CN_FIRST_NAME.add("岚风");
CN_FIRST_NAME.add("映冬");
CN_FIRST_NAME.add("霞英");
CN_FIRST_NAME.add("高轩");
CN_FIRST_NAME.add("善和");
CN_FIRST_NAME.add("琇芳");
CN_FIRST_NAME.add("凝旋");
CN_FIRST_NAME.add("半香");
CN_FIRST_NAME.add("念烟");
CN_FIRST_NAME.add("如风");
CN_FIRST_NAME.add("凌柏");
CN_FIRST_NAME.add("琇芬");
CN_FIRST_NAME.add("泰平");
CN_FIRST_NAME.add("俊明");
CN_FIRST_NAME.add("暄文");
CN_FIRST_NAME.add("瑾瑜");
CN_FIRST_NAME.add("丝娜");
CN_FIRST_NAME.add("铃语");
CN_FIRST_NAME.add("子惠");
CN_FIRST_NAME.add("明珠");
CN_FIRST_NAME.add("抒怀");
CN_FIRST_NAME.add("弘毅");
CN_FIRST_NAME.add("采梦");
CN_FIRST_NAME.add("从蓉");
CN_FIRST_NAME.add("景行");
CN_FIRST_NAME.add("慕晴");
CN_FIRST_NAME.add("瑾瑶");
CN_FIRST_NAME.add("安娜");
CN_FIRST_NAME.add("海之");
CN_FIRST_NAME.add("悦宜");
CN_FIRST_NAME.add("平心");
CN_FIRST_NAME.add("奇思");
CN_FIRST_NAME.add("绮烟");
CN_FIRST_NAME.add("秀兰");
CN_FIRST_NAME.add("安娴");
CN_FIRST_NAME.add("书兰");
CN_FIRST_NAME.add("洛妃");
CN_FIRST_NAME.add("俊晖");
CN_FIRST_NAME.add("昆锐");
CN_FIRST_NAME.add("翰采");
CN_FIRST_NAME.add("云水");
CN_FIRST_NAME.add("吟怀");
CN_FIRST_NAME.add("碧玉");
CN_FIRST_NAME.add("琼岚");
CN_FIRST_NAME.add("俊晤");
CN_FIRST_NAME.add("新美");
CN_FIRST_NAME.add("夏月");
CN_FIRST_NAME.add("问柳");
CN_FIRST_NAME.add("曼青");
CN_FIRST_NAME.add("丹雪");
CN_FIRST_NAME.add("情韵");
CN_FIRST_NAME.add("浩瀚");
CN_FIRST_NAME.add("华奥");
CN_FIRST_NAME.add("蝶梦");
CN_FIRST_NAME.add("天菱");
CN_FIRST_NAME.add("鸿晖");
CN_FIRST_NAME.add("璇玑");
CN_FIRST_NAME.add("皓君");
CN_FIRST_NAME.add("春兰");
CN_FIRST_NAME.add("忆雪");
CN_FIRST_NAME.add("齐敏");
CN_FIRST_NAME.add("灿灿");
CN_FIRST_NAME.add("娅楠");
CN_FIRST_NAME.add("芷容");
CN_FIRST_NAME.add("高澹");
CN_FIRST_NAME.add("真茹");
CN_FIRST_NAME.add("高达");
CN_FIRST_NAME.add("阳德");
CN_FIRST_NAME.add("梦菡");
CN_FIRST_NAME.add("淳美");
CN_FIRST_NAME.add("阳羽");
CN_FIRST_NAME.add("俊智");
CN_FIRST_NAME.add("星爵");
CN_FIRST_NAME.add("彦芝");
CN_FIRST_NAME.add("金枝");
CN_FIRST_NAME.add("梦菲");
CN_FIRST_NAME.add("灵凡");
CN_FIRST_NAME.add("海亦");
CN_FIRST_NAME.add("白雪");
CN_FIRST_NAME.add("恨荷");
CN_FIRST_NAME.add("秋灵");
CN_FIRST_NAME.add("雅丹");
CN_FIRST_NAME.add("雅丽");
CN_FIRST_NAME.add("姝丽");
CN_FIRST_NAME.add("可昕");
CN_FIRST_NAME.add("高远");
CN_FIRST_NAME.add("寄南");
CN_FIRST_NAME.add("茂勋");
CN_FIRST_NAME.add("忆霜");
CN_FIRST_NAME.add("代芙");
CN_FIRST_NAME.add("星剑");
CN_FIRST_NAME.add("丽雅");
CN_FIRST_NAME.add("振海");
CN_FIRST_NAME.add("春冬");
CN_FIRST_NAME.add("英锐");
CN_FIRST_NAME.add("英哲");
CN_FIRST_NAME.add("浩邈");
CN_FIRST_NAME.add("乐和");
CN_FIRST_NAME.add("婉慧");
CN_FIRST_NAME.add("乐咏");
CN_FIRST_NAME.add("璇珠");
CN_FIRST_NAME.add("尔槐");
CN_FIRST_NAME.add("逸");
CN_FIRST_NAME.add("智杰");
CN_FIRST_NAME.add("代芹");
CN_FIRST_NAME.add("志用");
CN_FIRST_NAME.add("书凝");
CN_FIRST_NAME.add("建修");
CN_FIRST_NAME.add("寒凝");
CN_FIRST_NAME.add("问梅");
CN_FIRST_NAME.add("永长");
CN_FIRST_NAME.add("新翰");
CN_FIRST_NAME.add("绮兰");
CN_FIRST_NAME.add("微婉");
CN_FIRST_NAME.add("痴柏");
CN_FIRST_NAME.add("昕珏");
CN_FIRST_NAME.add("翠琴");
CN_FIRST_NAME.add("春燕");
CN_FIRST_NAME.add("梓暄");
CN_FIRST_NAME.add("南风");
CN_FIRST_NAME.add("香雪");
CN_FIRST_NAME.add("逸馨");
CN_FIRST_NAME.add("巧兰");
CN_FIRST_NAME.add("碧琴");
CN_FIRST_NAME.add("碧琳");
CN_FIRST_NAME.add("筠心");
CN_FIRST_NAME.add("若雁");
CN_FIRST_NAME.add("如馨");
CN_FIRST_NAME.add("明钰");
CN_FIRST_NAME.add("芃芃");
CN_FIRST_NAME.add("项禹");
CN_FIRST_NAME.add("高逸");
CN_FIRST_NAME.add("和玉");
CN_FIRST_NAME.add("澎湃");
CN_FIRST_NAME.add("盼柳");
CN_FIRST_NAME.add("经略");
CN_FIRST_NAME.add("从蕾");
CN_FIRST_NAME.add("曼音");
CN_FIRST_NAME.add("楚云");
CN_FIRST_NAME.add("雅云");
CN_FIRST_NAME.add("奇胜");
CN_FIRST_NAME.add("夜春");
CN_FIRST_NAME.add("海伦");
CN_FIRST_NAME.add("云泽");
CN_FIRST_NAME.add("思洁");
CN_FIRST_NAME.add("紫桐");
CN_FIRST_NAME.add("骏奇");
CN_FIRST_NAME.add("悠素");
CN_FIRST_NAME.add("耘涛");
CN_FIRST_NAME.add("忻然");
CN_FIRST_NAME.add("沛槐");
CN_FIRST_NAME.add("逸秀");
CN_FIRST_NAME.add("琇莹");
CN_FIRST_NAME.add("颐真");
CN_FIRST_NAME.add("运晟");
CN_FIRST_NAME.add("意远");
CN_FIRST_NAME.add("越泽");
CN_FIRST_NAME.add("高邈");
CN_FIRST_NAME.add("文敏");
CN_FIRST_NAME.add("骏祥");
CN_FIRST_NAME.add("英喆");
CN_FIRST_NAME.add("朵儿");
CN_FIRST_NAME.add("明哲");
CN_FIRST_NAME.add("香露");
CN_FIRST_NAME.add("鸿朗");
CN_FIRST_NAME.add("梅梅");
CN_FIRST_NAME.add("康顺");
CN_FIRST_NAME.add("姣丽");
CN_FIRST_NAME.add("华婉");
CN_FIRST_NAME.add("飞跃");
CN_FIRST_NAME.add("运虹");
CN_FIRST_NAME.add("骊娜");
CN_FIRST_NAME.add("骊娟");
CN_FIRST_NAME.add("乐生");
CN_FIRST_NAME.add("平惠");
CN_FIRST_NAME.add("子舒");
CN_FIRST_NAME.add("天蓉");
CN_FIRST_NAME.add("俊材");
CN_FIRST_NAME.add("璎玑");
CN_FIRST_NAME.add("幻翠");
CN_FIRST_NAME.add("湘君");
CN_FIRST_NAME.add("夏柳");
CN_FIRST_NAME.add("笑槐");
CN_FIRST_NAME.add("巧凡");
CN_FIRST_NAME.add("涵柳");
CN_FIRST_NAME.add("正信");
CN_FIRST_NAME.add("兴发");
CN_FIRST_NAME.add("永嘉");
CN_FIRST_NAME.add("德馨");
CN_FIRST_NAME.add("天蓝");
CN_FIRST_NAME.add("浩然");
CN_FIRST_NAME.add("叶春");
CN_FIRST_NAME.add("文斌");
CN_FIRST_NAME.add("嫔然");
CN_FIRST_NAME.add("玉华");
CN_FIRST_NAME.add("俊杰");
CN_FIRST_NAME.add("初彤");
CN_FIRST_NAME.add("依波");
CN_FIRST_NAME.add("贞婉");
CN_FIRST_NAME.add("寄琴");
CN_FIRST_NAME.add("安筠");
CN_FIRST_NAME.add("迎曼");
CN_FIRST_NAME.add("斌蔚");
CN_FIRST_NAME.add("星华");
CN_FIRST_NAME.add("仪芳");
CN_FIRST_NAME.add("语彤");
CN_FIRST_NAME.add("飞丹");
CN_FIRST_NAME.add("和同");
CN_FIRST_NAME.add("昂雄");
CN_FIRST_NAME.add("骊婧");
CN_FIRST_NAME.add("安宁");
CN_FIRST_NAME.add("山彤");
CN_FIRST_NAME.add("痴梅");
CN_FIRST_NAME.add("端丽");
CN_FIRST_NAME.add("涵桃");
CN_FIRST_NAME.add("艳蕊");
CN_FIRST_NAME.add("起运");
CN_FIRST_NAME.add("冉冉");
CN_FIRST_NAME.add("安安");
CN_FIRST_NAME.add("幼怡");
CN_FIRST_NAME.add("莉莉");
CN_FIRST_NAME.add("凝蝶");
CN_FIRST_NAME.add("昊嘉");
CN_FIRST_NAME.add("明喆");
CN_FIRST_NAME.add("思涵");
CN_FIRST_NAME.add("涵衍");
CN_FIRST_NAME.add("安宜");
CN_FIRST_NAME.add("寄瑶");
CN_FIRST_NAME.add("赫然");
CN_FIRST_NAME.add("康复");
CN_FIRST_NAME.add("弘济");
CN_FIRST_NAME.add("骊婷");
CN_FIRST_NAME.add("燕桦");
CN_FIRST_NAME.add("昆皓");
CN_FIRST_NAME.add("宇寰");
CN_FIRST_NAME.add("骊媛");
CN_FIRST_NAME.add("靖巧");
CN_FIRST_NAME.add("玉环");
CN_FIRST_NAME.add("佩玉");
CN_FIRST_NAME.add("芊芊");
CN_FIRST_NAME.add("醉冬");
CN_FIRST_NAME.add("颀秀");
CN_FIRST_NAME.add("宛妙");
CN_FIRST_NAME.add("艳蕙");
CN_FIRST_NAME.add("文昂");
CN_FIRST_NAME.add("玉珂");
CN_FIRST_NAME.add("冰洁");
CN_FIRST_NAME.add("安容");
CN_FIRST_NAME.add("安寒");
CN_FIRST_NAME.add("子芸");
CN_FIRST_NAME.add("语心");
CN_FIRST_NAME.add("以莲");
CN_FIRST_NAME.add("文昌");
CN_FIRST_NAME.add("梦蕊");
CN_FIRST_NAME.add("初翠");
CN_FIRST_NAME.add("仲舒");
CN_FIRST_NAME.add("长霞");
CN_FIRST_NAME.add("妙音");
CN_FIRST_NAME.add("昆雄");
CN_FIRST_NAME.add("思淼");
CN_FIRST_NAME.add("文星");
CN_FIRST_NAME.add("天薇");
CN_FIRST_NAME.add("半安");
CN_FIRST_NAME.add("向荣");
CN_FIRST_NAME.add("灵卉");
CN_FIRST_NAME.add("云淡");
CN_FIRST_NAME.add("司晨");
CN_FIRST_NAME.add("涵梅");
CN_FIRST_NAME.add("秀华");
CN_FIRST_NAME.add("惜雪");
CN_FIRST_NAME.add("谷雪");
CN_FIRST_NAME.add("建元");
CN_FIRST_NAME.add("千山");
CN_FIRST_NAME.add("清绮");
CN_FIRST_NAME.add("奇致");
CN_FIRST_NAME.add("澄邈");
CN_FIRST_NAME.add("雅达");
CN_FIRST_NAME.add("柔绚");
CN_FIRST_NAME.add("斌斌");
CN_FIRST_NAME.add("舒兰");
CN_FIRST_NAME.add("佩珍");
CN_FIRST_NAME.add("高兴");
CN_FIRST_NAME.add("和璧");
CN_FIRST_NAME.add("雅辰");
CN_FIRST_NAME.add("宛秋");
CN_FIRST_NAME.add("元驹");
CN_FIRST_NAME.add("莎莉");
CN_FIRST_NAME.add("妍妍");
CN_FIRST_NAME.add("梓柔");
CN_FIRST_NAME.add("海逸");
CN_FIRST_NAME.add("嫚儿");
CN_FIRST_NAME.add("银柳");
CN_FIRST_NAME.add("运杰");
CN_FIRST_NAME.add("娅欣");
CN_FIRST_NAME.add("凯旋");
CN_FIRST_NAME.add("晨欣");
CN_FIRST_NAME.add("书南");
CN_FIRST_NAME.add("访文");
CN_FIRST_NAME.add("文景");
CN_FIRST_NAME.add("春华");
CN_FIRST_NAME.add("暮芸");
CN_FIRST_NAME.add("思义");
CN_FIRST_NAME.add("玉琲");
CN_FIRST_NAME.add("冰海");
CN_FIRST_NAME.add("莎莎");
CN_FIRST_NAME.add("睿好");
CN_FIRST_NAME.add("弘深");
CN_FIRST_NAME.add("勇毅");
CN_FIRST_NAME.add("宵雨");
CN_FIRST_NAME.add("浩初");
CN_FIRST_NAME.add("慕梅");
CN_FIRST_NAME.add("驰鸿");
CN_FIRST_NAME.add("文虹");
CN_FIRST_NAME.add("彩萱");
CN_FIRST_NAME.add("梦旋");
CN_FIRST_NAME.add("慧晨");
CN_FIRST_NAME.add("恨蕊");
CN_FIRST_NAME.add("灵珊");
CN_FIRST_NAME.add("寻云");
CN_FIRST_NAME.add("怜云");
CN_FIRST_NAME.add("白风");
CN_FIRST_NAME.add("慧智");
CN_FIRST_NAME.add("经国");
CN_FIRST_NAME.add("琴心");
CN_FIRST_NAME.add("雅逸");
CN_FIRST_NAME.add("布侬");
CN_FIRST_NAME.add("小谷");
CN_FIRST_NAME.add("弘业");
CN_FIRST_NAME.add("素欣");
CN_FIRST_NAME.add("斐斐");
CN_FIRST_NAME.add("源源");
CN_FIRST_NAME.add("志国");
CN_FIRST_NAME.add("嘉月");
CN_FIRST_NAME.add("宏富");
CN_FIRST_NAME.add("玉瑾");
CN_FIRST_NAME.add("思源");
CN_FIRST_NAME.add("思云");
CN_FIRST_NAME.add("梦易");
CN_FIRST_NAME.add("兴生");
CN_FIRST_NAME.add("思溪");
CN_FIRST_NAME.add("华容");
CN_FIRST_NAME.add("奥维");
CN_FIRST_NAME.add("燕楠");
CN_FIRST_NAME.add("晓丝");
CN_FIRST_NAME.add("绮南");
CN_FIRST_NAME.add("妙颜");
CN_FIRST_NAME.add("依丝");
CN_FIRST_NAME.add("阳舒");
CN_FIRST_NAME.add("弘丽");
CN_FIRST_NAME.add("阳成");
CN_FIRST_NAME.add("书双");
CN_FIRST_NAME.add("云溪");
CN_FIRST_NAME.add("媛女");
CN_FIRST_NAME.add("和畅");
CN_FIRST_NAME.add("云亭");
CN_FIRST_NAME.add("嘉木");
CN_FIRST_NAME.add("文曜");
CN_FIRST_NAME.add("弘义");
CN_FIRST_NAME.add("心香");
CN_FIRST_NAME.add("星瑶");
CN_FIRST_NAME.add("霞文");
CN_FIRST_NAME.add("白夏");
CN_FIRST_NAME.add("曼妮");
CN_FIRST_NAME.add("琳怡");
CN_FIRST_NAME.add("翠阳");
CN_FIRST_NAME.add("昌盛");
CN_FIRST_NAME.add("觅荷");
CN_FIRST_NAME.add("怡乐");
CN_FIRST_NAME.add("代蓝");
CN_FIRST_NAME.add("雅健");
CN_FIRST_NAME.add("清心");
CN_FIRST_NAME.add("绮玉");
CN_FIRST_NAME.add("元魁");
CN_FIRST_NAME.add("平良");
CN_FIRST_NAME.add("夜柳");
CN_FIRST_NAME.add("绿兰");
CN_FIRST_NAME.add("善静");
CN_FIRST_NAME.add("歌吹");
CN_FIRST_NAME.add("天晴");
CN_FIRST_NAME.add("凝梦");
CN_FIRST_NAME.add("迎梅");
CN_FIRST_NAME.add("茹云");
CN_FIRST_NAME.add("彤蕊");
CN_FIRST_NAME.add("吉敏");
CN_FIRST_NAME.add("良朋");
CN_FIRST_NAME.add("靓影");
CN_FIRST_NAME.add("津童");
CN_FIRST_NAME.add("睿姿");
CN_FIRST_NAME.add("冬亦");
CN_FIRST_NAME.add("胤雅");
CN_FIRST_NAME.add("念珍");
CN_FIRST_NAME.add("宾白");
CN_FIRST_NAME.add("高爽");
CN_FIRST_NAME.add("书君");
CN_FIRST_NAME.add("念双");
CN_FIRST_NAME.add("如容");
CN_FIRST_NAME.add("书琴");
CN_FIRST_NAME.add("凡桃");
CN_FIRST_NAME.add("慧月");
CN_FIRST_NAME.add("梦晨");
CN_FIRST_NAME.add("韵诗");
CN_FIRST_NAME.add("冰之");
CN_FIRST_NAME.add("子菡");
CN_FIRST_NAME.add("依云");
CN_FIRST_NAME.add("弘亮");
CN_FIRST_NAME.add("瀚彭");
CN_FIRST_NAME.add("柔怀");
CN_FIRST_NAME.add("香天");
CN_FIRST_NAME.add("春琳");
CN_FIRST_NAME.add("璞玉");
CN_FIRST_NAME.add("海儿");
CN_FIRST_NAME.add("芮美");
CN_FIRST_NAME.add("清怡");
CN_FIRST_NAME.add("绿凝");
CN_FIRST_NAME.add("承教");
CN_FIRST_NAME.add("嫣然");
CN_FIRST_NAME.add("碧白");
CN_FIRST_NAME.add("丹秋");
CN_FIRST_NAME.add("德宇");
CN_FIRST_NAME.add("英睿");
CN_FIRST_NAME.add("曼婉");
CN_FIRST_NAME.add("敏丽");
CN_FIRST_NAME.add("忆秋");
CN_FIRST_NAME.add("暖暖");
CN_FIRST_NAME.add("良材");
CN_FIRST_NAME.add("颖颖");
CN_FIRST_NAME.add("乐圣");
CN_FIRST_NAME.add("俊楚");
CN_FIRST_NAME.add("俊楠");
CN_FIRST_NAME.add("元容");
CN_FIRST_NAME.add("雁兰");
CN_FIRST_NAME.add("白秋");
CN_FIRST_NAME.add("夜梅");
CN_FIRST_NAME.add("德容");
CN_FIRST_NAME.add("子萱");
CN_FIRST_NAME.add("秋华");
CN_FIRST_NAME.add("蓝尹");
CN_FIRST_NAME.add("醉卉");
CN_FIRST_NAME.add("攸然");
CN_FIRST_NAME.add("天曼");
CN_FIRST_NAME.add("锐藻");
CN_FIRST_NAME.add("辰沛");
CN_FIRST_NAME.add("文林");
CN_FIRST_NAME.add("思佳");
CN_FIRST_NAME.add("夜梦");
CN_FIRST_NAME.add("泽恩");
CN_FIRST_NAME.add("雨泽");
CN_FIRST_NAME.add("望雅");
CN_FIRST_NAME.add("绮琴");
CN_FIRST_NAME.add("成化");
CN_FIRST_NAME.add("访曼");
CN_FIRST_NAME.add("弘伟");
CN_FIRST_NAME.add("以蕊");
CN_FIRST_NAME.add("莘莘");
CN_FIRST_NAME.add("秋玉");
CN_FIRST_NAME.add("水风");
CN_FIRST_NAME.add("正初");
CN_FIRST_NAME.add("海冬");
CN_FIRST_NAME.add("浩博");
CN_FIRST_NAME.add("梓楠");
CN_FIRST_NAME.add("嘉树");
CN_FIRST_NAME.add("德寿");
CN_FIRST_NAME.add("文柏");
CN_FIRST_NAME.add("同方");
CN_FIRST_NAME.add("新苗");
CN_FIRST_NAME.add("修敏");
CN_FIRST_NAME.add("翠霜");
CN_FIRST_NAME.add("月天");
CN_FIRST_NAME.add("念瑶");
CN_FIRST_NAME.add("熙熙");
CN_FIRST_NAME.add("宛筠");
CN_FIRST_NAME.add("梦月");
CN_FIRST_NAME.add("英韶");
CN_FIRST_NAME.add("香馨");
CN_FIRST_NAME.add("吉星");
CN_FIRST_NAME.add("桂华");
CN_FIRST_NAME.add("琇晶");
CN_FIRST_NAME.add("博学");
CN_FIRST_NAME.add("海凡");
CN_FIRST_NAME.add("静美");
CN_FIRST_NAME.add("宏峻");
CN_FIRST_NAME.add("丽姝");
CN_FIRST_NAME.add("岚岚");
CN_FIRST_NAME.add("清悦");
CN_FIRST_NAME.add("天材");
CN_FIRST_NAME.add("昆颉");
CN_FIRST_NAME.add("秋珊");
CN_FIRST_NAME.add("爰美");
CN_FIRST_NAME.add("雁凡");
CN_FIRST_NAME.add("思远");
CN_FIRST_NAME.add("修文");
CN_FIRST_NAME.add("梓榆");
CN_FIRST_NAME.add("易真");
CN_FIRST_NAME.add("思迪");
CN_FIRST_NAME.add("朝雨");
CN_FIRST_NAME.add("高卓");
CN_FIRST_NAME.add("文栋");
CN_FIRST_NAME.add("琼怡");
CN_FIRST_NAME.add("丽姿");
CN_FIRST_NAME.add("博简");
CN_FIRST_NAME.add("彦昌");
CN_FIRST_NAME.add("秋双");
CN_FIRST_NAME.add("琼思");
CN_FIRST_NAME.add("璞瑜");
CN_FIRST_NAME.add("锐智");
CN_FIRST_NAME.add("冷之");
CN_FIRST_NAME.add("昕雨");
CN_FIRST_NAME.add("柔惠");
CN_FIRST_NAME.add("昭君");
CN_FIRST_NAME.add("阳荣");
CN_FIRST_NAME.add("怀玉");
CN_FIRST_NAME.add("昊硕");
CN_FIRST_NAME.add("泽惠");
CN_FIRST_NAME.add("博实");
CN_FIRST_NAME.add("以旋");
CN_FIRST_NAME.add("煜祺");
CN_FIRST_NAME.add("驰翰");
CN_FIRST_NAME.add("博容");
CN_FIRST_NAME.add("翔飞");
CN_FIRST_NAME.add("明知");
CN_FIRST_NAME.add("向薇");
CN_FIRST_NAME.add("向文");
CN_FIRST_NAME.add("建华");
CN_FIRST_NAME.add("傲丝");
CN_FIRST_NAME.add("康宁");
CN_FIRST_NAME.add("力勤");
CN_FIRST_NAME.add("芮悦");
CN_FIRST_NAME.add("乐音");
CN_FIRST_NAME.add("平莹");
CN_FIRST_NAME.add("雅凡");
CN_FIRST_NAME.add("成双");
CN_FIRST_NAME.add("璠瑜");
CN_FIRST_NAME.add("和雅");
CN_FIRST_NAME.add("萌阳");
CN_FIRST_NAME.add("霞月");
CN_FIRST_NAME.add("依辰");
CN_FIRST_NAME.add("康安");
CN_FIRST_NAME.add("彭薄");
CN_FIRST_NAME.add("新荣");
CN_FIRST_NAME.add("惜天");
CN_FIRST_NAME.add("颖馨");
CN_FIRST_NAME.add("玟玉");
CN_FIRST_NAME.add("含芙");
CN_FIRST_NAME.add("冷亦");
CN_FIRST_NAME.add("玲然");
CN_FIRST_NAME.add("妞妞");
CN_FIRST_NAME.add("云逸");
CN_FIRST_NAME.add("玄雅");
CN_FIRST_NAME.add("寄真");
CN_FIRST_NAME.add("娇洁");
CN_FIRST_NAME.add("悦心");
CN_FIRST_NAME.add("昕靓");
CN_FIRST_NAME.add("骞骞");
CN_FIRST_NAME.add("飞烟");
CN_FIRST_NAME.add("傲之");
CN_FIRST_NAME.add("仪文");
CN_FIRST_NAME.add("又亦");
CN_FIRST_NAME.add("高原");
CN_FIRST_NAME.add("旭尧");
CN_FIRST_NAME.add("陶宁");
CN_FIRST_NAME.add("杏儿");
CN_FIRST_NAME.add("星阑");
CN_FIRST_NAME.add("湛雨");
CN_FIRST_NAME.add("芝英");
CN_FIRST_NAME.add("妙婧");
CN_FIRST_NAME.add("采波");
CN_FIRST_NAME.add("修明");
CN_FIRST_NAME.add("浦和");
CN_FIRST_NAME.add("素洁");
CN_FIRST_NAME.add("陶宜");
CN_FIRST_NAME.add("俊誉");
CN_FIRST_NAME.add("峻熙");
CN_FIRST_NAME.add("颖秀");
CN_FIRST_NAME.add("婷美");
CN_FIRST_NAME.add("韵流");
CN_FIRST_NAME.add("安平");
CN_FIRST_NAME.add("曼安");
CN_FIRST_NAME.add("恨蝶");
CN_FIRST_NAME.add("子蕙");
CN_FIRST_NAME.add("兴国");
CN_FIRST_NAME.add("听芹");
CN_FIRST_NAME.add("昊磊");
CN_FIRST_NAME.add("旻骞");
CN_FIRST_NAME.add("白竹");
CN_FIRST_NAME.add("吉月");
CN_FIRST_NAME.add("傲云");
CN_FIRST_NAME.add("平萱");
CN_FIRST_NAME.add("小之");
CN_FIRST_NAME.add("向明");
CN_FIRST_NAME.add("英飙");
CN_FIRST_NAME.add("珍丽");
CN_FIRST_NAME.add("雅爱");
CN_FIRST_NAME.add("映阳");
CN_FIRST_NAME.add("静恬");
CN_FIRST_NAME.add("令暎");
CN_FIRST_NAME.add("以晴");
CN_FIRST_NAME.add("湛霞");
CN_FIRST_NAME.add("伟彦");
CN_FIRST_NAME.add("曼容");
CN_FIRST_NAME.add("惜香");
CN_FIRST_NAME.add("心宜");
CN_FIRST_NAME.add("布凡");
CN_FIRST_NAME.add("悦怡");
CN_FIRST_NAME.add("其雨");
CN_FIRST_NAME.add("飞光");
CN_FIRST_NAME.add("子薇");
CN_FIRST_NAME.add("亦丝");
CN_FIRST_NAME.add("晨涛");
CN_FIRST_NAME.add("飞兰");
CN_FIRST_NAME.add("诗蕊");
CN_FIRST_NAME.add("绍祺");
CN_FIRST_NAME.add("欣笑");
CN_FIRST_NAME.add("敏达");
CN_FIRST_NAME.add("冬灵");
CN_FIRST_NAME.add("山芙");
CN_FIRST_NAME.add("安康");
CN_FIRST_NAME.add("典雅");
CN_FIRST_NAME.add("和静");
CN_FIRST_NAME.add("歌阑");
CN_FIRST_NAME.add("萍雅");
CN_FIRST_NAME.add("若骞");
CN_FIRST_NAME.add("怜烟");
CN_FIRST_NAME.add("灵阳");
CN_FIRST_NAME.add("梦桃");
CN_FIRST_NAME.add("风华");
CN_FIRST_NAME.add("萧玉");
CN_FIRST_NAME.add("昊天");
CN_FIRST_NAME.add("湛静");
CN_FIRST_NAME.add("成周");
CN_FIRST_NAME.add("建同");
CN_FIRST_NAME.add("曼寒");
CN_FIRST_NAME.add("永福");
CN_FIRST_NAME.add("玄静");
CN_FIRST_NAME.add("谷秋");
CN_FIRST_NAME.add("梦桐");
CN_FIRST_NAME.add("流如");
CN_FIRST_NAME.add("思烟");
CN_FIRST_NAME.add("骞魁");
CN_FIRST_NAME.add("幼荷");
CN_FIRST_NAME.add("承望");
CN_FIRST_NAME.add("成和");
CN_FIRST_NAME.add("小溪");
CN_FIRST_NAME.add("正卿");
CN_FIRST_NAME.add("语芹");
CN_FIRST_NAME.add("向晨");
CN_FIRST_NAME.add("诗文");
CN_FIRST_NAME.add("优悠");
CN_FIRST_NAME.add("尔丝");
CN_FIRST_NAME.add("梧桐");
CN_FIRST_NAME.add("优悦");
CN_FIRST_NAME.add("忆安");
CN_FIRST_NAME.add("白筠");
CN_FIRST_NAME.add("晓灵");
CN_FIRST_NAME.add("倩美");
CN_FIRST_NAME.add("伟志");
CN_FIRST_NAME.add("长娟");
CN_FIRST_NAME.add("英奕");
CN_FIRST_NAME.add("诗蕾");
CN_FIRST_NAME.add("清懿");
CN_FIRST_NAME.add("刚捷");
CN_FIRST_NAME.add("悦恺");
CN_FIRST_NAME.add("凌波");
CN_FIRST_NAME.add("清舒");
CN_FIRST_NAME.add("亦云");
CN_FIRST_NAME.add("白安");
CN_FIRST_NAME.add("星雨");
CN_FIRST_NAME.add("飞燕");
CN_FIRST_NAME.add("林楠");
CN_FIRST_NAME.add("忻畅");
CN_FIRST_NAME.add("圣杰");
CN_FIRST_NAME.add("彦杉");
CN_FIRST_NAME.add("振凯");
CN_FIRST_NAME.add("映雁");
CN_FIRST_NAME.add("丹寒");
CN_FIRST_NAME.add("钰");
CN_FIRST_NAME.add("子明");
CN_FIRST_NAME.add("子昂");
CN_FIRST_NAME.add("家馨");
CN_FIRST_NAME.add("雁卉");
CN_FIRST_NAME.add("平蓝");
CN_FIRST_NAME.add("听荷");
CN_FIRST_NAME.add("映雪");
CN_FIRST_NAME.add("晏然");
CN_FIRST_NAME.add("乐天");
CN_FIRST_NAME.add("白容");
CN_FIRST_NAME.add("访梦");
CN_FIRST_NAME.add("景浩");
CN_FIRST_NAME.add("恨桃");
CN_FIRST_NAME.add("熙华");
CN_FIRST_NAME.add("暖梦");
CN_FIRST_NAME.add("书白");
CN_FIRST_NAME.add("箫笛");
CN_FIRST_NAME.add("晴波");
CN_FIRST_NAME.add("馨香");
CN_FIRST_NAME.add("和韵");
CN_FIRST_NAME.add("含莲");
CN_FIRST_NAME.add("琳芳");
CN_FIRST_NAME.add("安彤");
CN_FIRST_NAME.add("子晋");
CN_FIRST_NAME.add("秀隽");
CN_FIRST_NAME.add("桐华");
CN_FIRST_NAME.add("映真");
CN_FIRST_NAME.add("尔云");
CN_FIRST_NAME.add("梓欣");
CN_FIRST_NAME.add("幼菱");
CN_FIRST_NAME.add("英秀");
CN_FIRST_NAME.add("季萌");
CN_FIRST_NAME.add("孤菱");
CN_FIRST_NAME.add("秀雅");
CN_FIRST_NAME.add("听莲");
CN_FIRST_NAME.add("书雁");
CN_FIRST_NAME.add("曼岚");
CN_FIRST_NAME.add("韶丽");
CN_FIRST_NAME.add("丽容");
CN_FIRST_NAME.add("寻冬");
CN_FIRST_NAME.add("嘉言");
CN_FIRST_NAME.add("灵雨");
CN_FIRST_NAME.add("孤萍");
CN_FIRST_NAME.add("巍奕");
CN_FIRST_NAME.add("寒雁");
CN_FIRST_NAME.add("流婉");
CN_FIRST_NAME.add("奇文");
CN_FIRST_NAME.add("慕诗");
CN_FIRST_NAME.add("以松");
CN_FIRST_NAME.add("锦文");
CN_FIRST_NAME.add("依然");
CN_FIRST_NAME.add("丝微");
CN_FIRST_NAME.add("怡然");
CN_FIRST_NAME.add("弘光");
CN_FIRST_NAME.add("静慧");
CN_FIRST_NAME.add("雯丽");
CN_FIRST_NAME.add("幼萱");
CN_FIRST_NAME.add("芙蓉");
CN_FIRST_NAME.add("和硕");
CN_FIRST_NAME.add("音仪");
CN_FIRST_NAME.add("君昊");
CN_FIRST_NAME.add("修杰");
CN_FIRST_NAME.add("水竹");
CN_FIRST_NAME.add("寻凝");
CN_FIRST_NAME.add("清芬");
CN_FIRST_NAME.add("骊红");
CN_FIRST_NAME.add("星睿");
CN_FIRST_NAME.add("令枫");
CN_FIRST_NAME.add("丹山");
CN_FIRST_NAME.add("雨伯");
CN_FIRST_NAME.add("代柔");
CN_FIRST_NAME.add("润丽");
CN_FIRST_NAME.add("骞尧");
CN_FIRST_NAME.add("余妍");
CN_FIRST_NAME.add("觅晴");
CN_FIRST_NAME.add("安翔");
CN_FIRST_NAME.add("颜骏");
CN_FIRST_NAME.add("念雁");
CN_FIRST_NAME.add("舒畅");
CN_FIRST_NAME.add("和顺");
CN_FIRST_NAME.add("安志");
CN_FIRST_NAME.add("余馥");
CN_FIRST_NAME.add("盼波");
CN_FIRST_NAME.add("春雪");
CN_FIRST_NAME.add("俊语");
CN_FIRST_NAME.add("思凡");
CN_FIRST_NAME.add("春雨");
CN_FIRST_NAME.add("晓兰");
CN_FIRST_NAME.add("诗晗");
CN_FIRST_NAME.add("和颂");
CN_FIRST_NAME.add("高畅");
CN_FIRST_NAME.add("平文");
CN_FIRST_NAME.add("寄风");
CN_FIRST_NAME.add("玉韵");
CN_FIRST_NAME.add("玉石");
CN_FIRST_NAME.add("向松");
CN_FIRST_NAME.add("俊民");
CN_FIRST_NAME.add("芬芬");
CN_FIRST_NAME.add("家骏");
CN_FIRST_NAME.add("景中");
CN_FIRST_NAME.add("雪漫");
CN_FIRST_NAME.add("湛颖");
CN_FIRST_NAME.add("玉堂");
CN_FIRST_NAME.add("萍韵");
CN_FIRST_NAME.add("白山");
CN_FIRST_NAME.add("山菡");
CN_FIRST_NAME.add("温纶");
CN_FIRST_NAME.add("昊穹");
CN_FIRST_NAME.add("沈然");
CN_FIRST_NAME.add("阳文");
CN_FIRST_NAME.add("韶仪");
CN_FIRST_NAME.add("以柳");
CN_FIRST_NAME.add("嘉誉");
CN_FIRST_NAME.add("戈雅");
CN_FIRST_NAME.add("安怡");
CN_FIRST_NAME.add("斯文");
CN_FIRST_NAME.add("夏波");
CN_FIRST_NAME.add("弘量");
CN_FIRST_NAME.add("芳懿");
CN_FIRST_NAME.add("昊空");
CN_FIRST_NAME.add("新蕾");
CN_FIRST_NAME.add("元纬");
CN_FIRST_NAME.add("念真");
CN_FIRST_NAME.add("浩阔");
CN_FIRST_NAME.add("秋阳");
CN_FIRST_NAME.add("雅珺");
CN_FIRST_NAME.add("和风");
CN_FIRST_NAME.add("代桃");
CN_FIRST_NAME.add("今歌");
CN_FIRST_NAME.add("念霜");
CN_FIRST_NAME.add("念露");
CN_FIRST_NAME.add("华彩");
CN_FIRST_NAME.add("海瑶");
CN_FIRST_NAME.add("言心");
CN_FIRST_NAME.add("骏年");
CN_FIRST_NAME.add("雅可");
CN_FIRST_NAME.add("英媛");
CN_FIRST_NAME.add("凌丝");
CN_FIRST_NAME.add("新文");
CN_FIRST_NAME.add("晓凡");
CN_FIRST_NAME.add("冠玉");
CN_FIRST_NAME.add("梦槐");
CN_FIRST_NAME.add("叶欣");
CN_FIRST_NAME.add("晨潍");
CN_FIRST_NAME.add("依凝");
CN_FIRST_NAME.add("俊豪");
CN_FIRST_NAME.add("德庸");
CN_FIRST_NAME.add("雨信");
CN_FIRST_NAME.add("斯斯");
CN_FIRST_NAME.add("晓燕");
CN_FIRST_NAME.add("振华");
CN_FIRST_NAME.add("琼芳");
CN_FIRST_NAME.add("坚成");
CN_FIRST_NAME.add("问丝");
CN_FIRST_NAME.add("友灵");
CN_FIRST_NAME.add("岚彩");
CN_FIRST_NAME.add("振博");
CN_FIRST_NAME.add("惜筠");
CN_FIRST_NAME.add("阳旭");
CN_FIRST_NAME.add("冰冰");
CN_FIRST_NAME.add("华美");
CN_FIRST_NAME.add("代梅");
CN_FIRST_NAME.add("绮露");
CN_FIRST_NAME.add("痴海");
CN_FIRST_NAME.add("晨轩");
CN_FIRST_NAME.add("旭鹏");
CN_FIRST_NAME.add("翰音");
CN_FIRST_NAME.add("溪澈");
CN_FIRST_NAME.add("元绿");
CN_FIRST_NAME.add("平春");
CN_FIRST_NAME.add("运诚");
CN_FIRST_NAME.add("秋白");
CN_FIRST_NAME.add("雅琴");
CN_FIRST_NAME.add("昕妤");
CN_FIRST_NAME.add("歌韵");
CN_FIRST_NAME.add("妮娜");
CN_FIRST_NAME.add("令梓");
CN_FIRST_NAME.add("令梅");
CN_FIRST_NAME.add("如彤");
CN_FIRST_NAME.add("胤骞");
CN_FIRST_NAME.add("灵韵");
CN_FIRST_NAME.add("玮琪");
CN_FIRST_NAME.add("香岚");
CN_FIRST_NAME.add("北晶");
CN_FIRST_NAME.add("琼英");
CN_FIRST_NAME.add("冰凡");
CN_FIRST_NAME.add("若山");
CN_FIRST_NAME.add("翔宇");
CN_FIRST_NAME.add("晨辰");
CN_FIRST_NAME.add("永宁");
CN_FIRST_NAME.add("晴丽");
CN_FIRST_NAME.add("顺美");
CN_FIRST_NAME.add("逸美");
CN_FIRST_NAME.add("觅松");
CN_FIRST_NAME.add("高阳");
CN_FIRST_NAME.add("平晓");
CN_FIRST_NAME.add("瑞绣");
CN_FIRST_NAME.add("昆宇");
CN_FIRST_NAME.add("玲玲");
CN_FIRST_NAME.add("开畅");
CN_FIRST_NAME.add("玲珑");
CN_FIRST_NAME.add("宜年");
CN_FIRST_NAME.add("嘉歆");
CN_FIRST_NAME.add("骊美");
CN_FIRST_NAME.add("清莹");
CN_FIRST_NAME.add("永安");
CN_FIRST_NAME.add("紫丝");
CN_FIRST_NAME.add("优扬");
CN_FIRST_NAME.add("浩皛");
CN_FIRST_NAME.add("志学");
CN_FIRST_NAME.add("江雪");
CN_FIRST_NAME.add("华翰");
CN_FIRST_NAME.add("初蓝");
CN_FIRST_NAME.add("语蓉");
CN_FIRST_NAME.add("银河");
CN_FIRST_NAME.add("芳芳");
CN_FIRST_NAME.add("静芙");
CN_FIRST_NAME.add("含蕊");
CN_FIRST_NAME.add("晨濡");
CN_FIRST_NAME.add("璇娟");
CN_FIRST_NAME.add("密如");
CN_FIRST_NAME.add("惜寒");
CN_FIRST_NAME.add("映颖");
CN_FIRST_NAME.add("又儿");
CN_FIRST_NAME.add("涵涤");
CN_FIRST_NAME.add("伟懋");
CN_FIRST_NAME.add("柳思");
CN_FIRST_NAME.add("如心");
CN_FIRST_NAME.add("元彤");
CN_FIRST_NAME.add("岚翠");
CN_FIRST_NAME.add("鸿波");
CN_FIRST_NAME.add("芳苓");
CN_FIRST_NAME.add("俊贤");
CN_FIRST_NAME.add("阳晖");
CN_FIRST_NAME.add("野云");
CN_FIRST_NAME.add("锦曦");
CN_FIRST_NAME.add("康平");
CN_FIRST_NAME.add("闲丽");
CN_FIRST_NAME.add("乐章");
CN_FIRST_NAME.add("乐童");
CN_FIRST_NAME.add("涵润");
CN_FIRST_NAME.add("玲琅");
CN_FIRST_NAME.add("雨灵");
CN_FIRST_NAME.add("婉柔");
CN_FIRST_NAME.add("茗雪");
CN_FIRST_NAME.add("兰娜");
CN_FIRST_NAME.add("涵涵");
CN_FIRST_NAME.add("怜南");
CN_FIRST_NAME.add("昊宇");
CN_FIRST_NAME.add("盼丹");
CN_FIRST_NAME.add("薇歌");
CN_FIRST_NAME.add("含文");
CN_FIRST_NAME.add("成益");
CN_FIRST_NAME.add("翰墨");
CN_FIRST_NAME.add("闳丽");
CN_FIRST_NAME.add("黛娥");
CN_FIRST_NAME.add("元龙");
CN_FIRST_NAME.add("飞双");
CN_FIRST_NAME.add("飞珍");
CN_FIRST_NAME.add("觅柔");
CN_FIRST_NAME.add("向梦");
CN_FIRST_NAME.add("宏恺");
CN_FIRST_NAME.add("梓洁");
CN_FIRST_NAME.add("幼旋");
CN_FIRST_NAME.add("嘉许");
CN_FIRST_NAME.add("迎波");
CN_FIRST_NAME.add("瑞彩");
CN_FIRST_NAME.add("傲儿");
CN_FIRST_NAME.add("思卉");
CN_FIRST_NAME.add("新晴");
CN_FIRST_NAME.add("建白");
CN_FIRST_NAME.add("秋露");
CN_FIRST_NAME.add("紫云");
CN_FIRST_NAME.add("永寿");
CN_FIRST_NAME.add("溶溶");
CN_FIRST_NAME.add("怀雁");
CN_FIRST_NAME.add("凝洁");
CN_FIRST_NAME.add("玲琳");
CN_FIRST_NAME.add("蕴涵");
CN_FIRST_NAME.add("鹤梦");
CN_FIRST_NAME.add("贞怡");
CN_FIRST_NAME.add("瑶岑");
CN_FIRST_NAME.add("博延");
CN_FIRST_NAME.add("思博");
CN_FIRST_NAME.add("芬菲");
CN_FIRST_NAME.add("秀颖");
CN_FIRST_NAME.add("智渊");
CN_FIRST_NAME.add("元德");
CN_FIRST_NAME.add("芳荃");
CN_FIRST_NAME.add("学文");
CN_FIRST_NAME.add("语蕊");
CN_FIRST_NAME.add("诗柳");
CN_FIRST_NAME.add("睿广");
CN_FIRST_NAME.add("芳茵");
CN_FIRST_NAME.add("靖荷");
CN_FIRST_NAME.add("逸思");
CN_FIRST_NAME.add("弘化");
CN_FIRST_NAME.add("景辉");
CN_FIRST_NAME.add("元忠");
CN_FIRST_NAME.add("景澄");
CN_FIRST_NAME.add("高雅");
CN_FIRST_NAME.add("翰飞");
CN_FIRST_NAME.add("阳曦");
CN_FIRST_NAME.add("映天");
CN_FIRST_NAME.add("长岳");
CN_FIRST_NAME.add("伟才");
CN_FIRST_NAME.add("桃雨");
CN_FIRST_NAME.add("芸芸");
CN_FIRST_NAME.add("才俊");
CN_FIRST_NAME.add("天欣");
CN_FIRST_NAME.add("旭彬");
CN_FIRST_NAME.add("冬卉");
CN_FIRST_NAME.add("夏之");
CN_FIRST_NAME.add("阳曜");
CN_FIRST_NAME.add("芷若");
CN_FIRST_NAME.add("雅唱");
CN_FIRST_NAME.add("歌飞");
CN_FIRST_NAME.add("晶滢");
CN_FIRST_NAME.add("运洁");
CN_FIRST_NAME.add("怜珊");
CN_FIRST_NAME.add("宏胜");
CN_FIRST_NAME.add("蕙兰");
CN_FIRST_NAME.add("志尚");
CN_FIRST_NAME.add("湛娟");
CN_FIRST_NAME.add("嘉谊");
CN_FIRST_NAME.add("凡波");
CN_FIRST_NAME.add("语薇");
CN_FIRST_NAME.add("方方");
CN_FIRST_NAME.add("乐安");
CN_FIRST_NAME.add("傲冬");
CN_FIRST_NAME.add("凝海");
CN_FIRST_NAME.add("元思");
CN_FIRST_NAME.add("莹莹");
CN_FIRST_NAME.add("雅畅");
CN_FIRST_NAME.add("凯歌");
CN_FIRST_NAME.add("国源");
CN_FIRST_NAME.add("寻双");
CN_FIRST_NAME.add("新曦");
CN_FIRST_NAME.add("怜双");
CN_FIRST_NAME.add("芸若");
CN_FIRST_NAME.add("正阳");
CN_FIRST_NAME.add("尔烟");
CN_FIRST_NAME.add("菁英");
CN_FIRST_NAME.add("朗宁");
CN_FIRST_NAME.add("羽彤");
CN_FIRST_NAME.add("未央");
CN_FIRST_NAME.add("弘博");
CN_FIRST_NAME.add("飞瑶");
CN_FIRST_NAME.add("玄穆");
CN_FIRST_NAME.add("芸茗");
CN_FIRST_NAME.add("莺莺");
CN_FIRST_NAME.add("阳朔");
CN_FIRST_NAME.add("新月");
CN_FIRST_NAME.add("鑫鹏");
CN_FIRST_NAME.add("诗桃");
CN_FIRST_NAME.add("乐容");
CN_FIRST_NAME.add("平松");
CN_FIRST_NAME.add("寅骏");
CN_FIRST_NAME.add("轩秀");
CN_FIRST_NAME.add("妮子");
CN_FIRST_NAME.add("夏云");
CN_FIRST_NAME.add("慧语");
CN_FIRST_NAME.add("晓博");
CN_FIRST_NAME.add("乐家");
CN_FIRST_NAME.add("听春");
CN_FIRST_NAME.add("幼晴");
CN_FIRST_NAME.add("好慕");
CN_FIRST_NAME.add("迎海");
CN_FIRST_NAME.add("香巧");
CN_FIRST_NAME.add("丹红");
CN_FIRST_NAME.add("哲丽");
CN_FIRST_NAME.add("丰羽");
CN_FIRST_NAME.add("依玉");
CN_FIRST_NAME.add("珠轩");
CN_FIRST_NAME.add("雪儿");
CN_FIRST_NAME.add("珠佩");
CN_FIRST_NAME.add("宇航");
CN_FIRST_NAME.add("运浩");
CN_FIRST_NAME.add("弘厚");
CN_FIRST_NAME.add("芳菲");
CN_FIRST_NAME.add("梓涵");
CN_FIRST_NAME.add("海阳");
CN_FIRST_NAME.add("寻琴");
CN_FIRST_NAME.add("世英");
CN_FIRST_NAME.add("涵亮");
CN_FIRST_NAME.add("雨兰");
CN_FIRST_NAME.add("孤晴");
CN_FIRST_NAME.add("寒天");
CN_FIRST_NAME.add("元恺");
CN_FIRST_NAME.add("思琪");
CN_FIRST_NAME.add("景逸");
CN_FIRST_NAME.add("小凝");
CN_FIRST_NAME.add("昆峰");
CN_FIRST_NAME.add("映秋");
CN_FIRST_NAME.add("璇子");
CN_FIRST_NAME.add("宾实");
CN_FIRST_NAME.add("含景");
CN_FIRST_NAME.add("芷荷");
CN_FIRST_NAME.add("柔蔓");
CN_FIRST_NAME.add("熙阳");
CN_FIRST_NAME.add("隽雅");
CN_FIRST_NAME.add("思琳");
CN_FIRST_NAME.add("勇军");
CN_FIRST_NAME.add("如意");
CN_FIRST_NAME.add("蕊珠");
CN_FIRST_NAME.add("依珊");
CN_FIRST_NAME.add("伟茂");
CN_FIRST_NAME.add("睿彤");
CN_FIRST_NAME.add("巧风");
CN_FIRST_NAME.add("振锐");
CN_FIRST_NAME.add("正雅");
CN_FIRST_NAME.add("添智");
CN_FIRST_NAME.add("雪兰");
CN_FIRST_NAME.add("向槐");
CN_FIRST_NAME.add("溪儿");
CN_FIRST_NAME.add("光耀");
CN_FIRST_NAME.add("从波");
CN_FIRST_NAME.add("晶辉");
CN_FIRST_NAME.add("学智");
CN_FIRST_NAME.add("秀妮");
CN_FIRST_NAME.add("鹏池");
CN_FIRST_NAME.add("曼彤");
CN_FIRST_NAME.add("灵秀");
CN_FIRST_NAME.add("雨凝");
CN_FIRST_NAME.add("敏博");
CN_FIRST_NAME.add("智伟");
CN_FIRST_NAME.add("凝丝");
CN_FIRST_NAME.add("海白");
CN_FIRST_NAME.add("新林");
CN_FIRST_NAME.add("康德");
CN_FIRST_NAME.add("博耘");
CN_FIRST_NAME.add("娟丽");
CN_FIRST_NAME.add("凝丹");
CN_FIRST_NAME.add("灵秋");
CN_FIRST_NAME.add("初晴");
CN_FIRST_NAME.add("唱月");
CN_FIRST_NAME.add("亦凝");
CN_FIRST_NAME.add("雨燕");
CN_FIRST_NAME.add("德惠");
CN_FIRST_NAME.add("巧夏");
CN_FIRST_NAME.add("娇然");
CN_FIRST_NAME.add("沛儿");
CN_FIRST_NAME.add("易容");
CN_FIRST_NAME.add("语晨");
CN_FIRST_NAME.add("寒香");
CN_FIRST_NAME.add("开霁");
CN_FIRST_NAME.add("高韵");
CN_FIRST_NAME.add("菀菀");
CN_FIRST_NAME.add("正真");
CN_FIRST_NAME.add("怡君");
CN_FIRST_NAME.add("春妤");
CN_FIRST_NAME.add("尔冬");
CN_FIRST_NAME.add("雪冰");
CN_FIRST_NAME.add("睿德");
CN_FIRST_NAME.add("冰双");
CN_FIRST_NAME.add("冰珍");
CN_FIRST_NAME.add("子楠");
CN_FIRST_NAME.add("顺慈");
CN_FIRST_NAME.add("嘉泽");
CN_FIRST_NAME.add("红艳");
CN_FIRST_NAME.add("迎丝");
CN_FIRST_NAME.add("鸿云");
CN_FIRST_NAME.add("晗玥");
CN_FIRST_NAME.add("秋颖");
CN_FIRST_NAME.add("晓君");
CN_FIRST_NAME.add("新柔");
CN_FIRST_NAME.add("山晴");
CN_FIRST_NAME.add("乐山");
CN_FIRST_NAME.add("贤惠");
CN_FIRST_NAME.add("吉欣");
CN_FIRST_NAME.add("菁菁");
CN_FIRST_NAME.add("俊人");
CN_FIRST_NAME.add("恬欣");
CN_FIRST_NAME.add("依琴");
CN_FIRST_NAME.add("星驰");
CN_FIRST_NAME.add("丹彤");
CN_FIRST_NAME.add("正青");
CN_FIRST_NAME.add("俏丽");
CN_FIRST_NAME.add("秀娟");
CN_FIRST_NAME.add("梓云");
CN_FIRST_NAME.add("春姝");
CN_FIRST_NAME.add("忆彤");
CN_FIRST_NAME.add("森莉");
CN_FIRST_NAME.add("海雪");
CN_FIRST_NAME.add("凝云");
CN_FIRST_NAME.add("青文");
CN_FIRST_NAME.add("嘉赐");
CN_FIRST_NAME.add("睿思");
CN_FIRST_NAME.add("依瑶");
CN_FIRST_NAME.add("佳妍");
CN_FIRST_NAME.add("初曼");
CN_FIRST_NAME.add("荣轩");
CN_FIRST_NAME.add("和安");
CN_FIRST_NAME.add("兴学");
CN_FIRST_NAME.add("敏叡");
CN_FIRST_NAME.add("寄容");
CN_FIRST_NAME.add("弘和");
CN_FIRST_NAME.add("红英");
CN_FIRST_NAME.add("凡之");
CN_FIRST_NAME.add("怡和");
CN_FIRST_NAME.add("雁露");
CN_FIRST_NAME.add("怡璐");
CN_FIRST_NAME.add("秀婉");
CN_FIRST_NAME.add("景焕");
CN_FIRST_NAME.add("雅隽");
CN_FIRST_NAME.add("春娇");
CN_FIRST_NAME.add("晓瑶");
CN_FIRST_NAME.add("孤松");
CN_FIRST_NAME.add("宏才");
CN_FIRST_NAME.add("浩壤");
CN_FIRST_NAME.add("巧香");
CN_FIRST_NAME.add("和宜");
CN_FIRST_NAME.add("琳晨");
CN_FIRST_NAME.add("幻枫");
CN_FIRST_NAME.add("兴安");
CN_FIRST_NAME.add("瀚文");
CN_FIRST_NAME.add("绢子");
CN_FIRST_NAME.add("幼枫");
CN_FIRST_NAME.add("半芹");
CN_FIRST_NAME.add("文赋");
CN_FIRST_NAME.add("欣彩");
CN_FIRST_NAME.add("青旋");
CN_FIRST_NAME.add("欣彤");
CN_FIRST_NAME.add("逸致");
CN_FIRST_NAME.add("沛凝");
CN_FIRST_NAME.add("晗琴");
CN_FIRST_NAME.add("心思");
CN_FIRST_NAME.add("晶灵");
CN_FIRST_NAME.add("茂学");
CN_FIRST_NAME.add("心怡");
CN_FIRST_NAME.add("翠岚");
CN_FIRST_NAME.add("宏扬");
CN_FIRST_NAME.add("冷玉");
CN_FIRST_NAME.add("运乾");
CN_FIRST_NAME.add("睿聪");
CN_FIRST_NAME.add("欣美");
CN_FIRST_NAME.add("长平");
CN_FIRST_NAME.add("诗槐");
CN_FIRST_NAME.add("茂实");
CN_FIRST_NAME.add("丹翠");
CN_FIRST_NAME.add("宇荫");
CN_FIRST_NAME.add("鹏赋");
CN_FIRST_NAME.add("浩大");
CN_FIRST_NAME.add("秀媛");
CN_FIRST_NAME.add("友卉");
CN_FIRST_NAME.add("秀媚");
CN_FIRST_NAME.add("以欣");
CN_FIRST_NAME.add("幼柏");
CN_FIRST_NAME.add("新梅");
CN_FIRST_NAME.add("清昶");
CN_FIRST_NAME.add("嘉淑");
CN_FIRST_NAME.add("凯泽");
CN_FIRST_NAME.add("雅霜");
CN_FIRST_NAME.add("韫玉");
CN_FIRST_NAME.add("傲南");
CN_FIRST_NAME.add("叶丰");
CN_FIRST_NAME.add("初蝶");
CN_FIRST_NAME.add("听枫");
CN_FIRST_NAME.add("升荣");
CN_FIRST_NAME.add("香彤");
CN_FIRST_NAME.add("欣德");
CN_FIRST_NAME.add("芳蔼");
CN_FIRST_NAME.add("学林");
CN_FIRST_NAME.add("冷珍");
CN_FIRST_NAME.add("清晖");
CN_FIRST_NAME.add("夜云");
CN_FIRST_NAME.add("天泽");
CN_FIRST_NAME.add("芳蕤");
CN_FIRST_NAME.add("问儿");
CN_FIRST_NAME.add("驰文");
CN_FIRST_NAME.add("华芝");
CN_FIRST_NAME.add("安荷");
CN_FIRST_NAME.add("昆鹏");
CN_FIRST_NAME.add("飞阳");
CN_FIRST_NAME.add("叶丹");
CN_FIRST_NAME.add("白翠");
CN_FIRST_NAME.add("盈盈");
CN_FIRST_NAME.add("康胜");
CN_FIRST_NAME.add("痴灵");
CN_FIRST_NAME.add("若彤");
CN_FIRST_NAME.add("玉宇");
CN_FIRST_NAME.add("访波");
CN_FIRST_NAME.add("青易");
CN_FIRST_NAME.add("成天");
CN_FIRST_NAME.add("高飞");
CN_FIRST_NAME.add("芳蕙");
CN_FIRST_NAME.add("芷蓝");
CN_FIRST_NAME.add("鸿轩");
CN_FIRST_NAME.add("梦泽");
CN_FIRST_NAME.add("鹏海");
CN_FIRST_NAME.add("傲玉");
CN_FIRST_NAME.add("俊侠");
CN_FIRST_NAME.add("成礼");
CN_FIRST_NAME.add("美曼");
CN_FIRST_NAME.add("从丹");
CN_FIRST_NAME.add("醉香");
CN_FIRST_NAME.add("幻桃");
CN_FIRST_NAME.add("瀚昂");
CN_FIRST_NAME.add("雅静");
CN_FIRST_NAME.add("凌兰");
CN_FIRST_NAME.add("山蝶");
CN_FIRST_NAME.add("蓉蓉");
CN_FIRST_NAME.add("永年");
CN_FIRST_NAME.add("俊迈");
CN_FIRST_NAME.add("三春");
CN_FIRST_NAME.add("秀竹");
CN_FIRST_NAME.add("双玉");
CN_FIRST_NAME.add("恬谧");
CN_FIRST_NAME.add("语蝶");
CN_FIRST_NAME.add("骊艳");
CN_FIRST_NAME.add("俊达");
CN_FIRST_NAME.add("鹏涛");
CN_FIRST_NAME.add("雅青");
CN_FIRST_NAME.add("玉宸");
CN_FIRST_NAME.add("安莲");
CN_FIRST_NAME.add("星宇");
CN_FIRST_NAME.add("贞芳");
CN_FIRST_NAME.add("怡畅");
CN_FIRST_NAME.add("天赋");
CN_FIRST_NAME.add("鸿达");
CN_FIRST_NAME.add("飞白");
CN_FIRST_NAME.add("珊珊");
CN_FIRST_NAME.add("问兰");
CN_FIRST_NAME.add("震轩");
CN_FIRST_NAME.add("欣怡");
CN_FIRST_NAME.add("友珊");
CN_FIRST_NAME.add("宏茂");
CN_FIRST_NAME.add("俊远");
CN_FIRST_NAME.add("书竹");
CN_FIRST_NAME.add("语林");
CN_FIRST_NAME.add("初柔");
CN_FIRST_NAME.add("晓畅");
CN_FIRST_NAME.add("嘉丽");
CN_FIRST_NAME.add("淑贞");
CN_FIRST_NAME.add("幻梅");
CN_FIRST_NAME.add("哲瀚");
CN_FIRST_NAME.add("鸿运");
CN_FIRST_NAME.add("映安");
CN_FIRST_NAME.add("又琴");
CN_FIRST_NAME.add("昆纬");
CN_FIRST_NAME.add("鸿远");
CN_FIRST_NAME.add("可佳");
CN_FIRST_NAME.add("靖易");
CN_FIRST_NAME.add("欣怿");
CN_FIRST_NAME.add("永康");
CN_FIRST_NAME.add("含桃");
CN_FIRST_NAME.add("雨华");
CN_FIRST_NAME.add("春竹");
CN_FIRST_NAME.add("翰学");
CN_FIRST_NAME.add("昆纶");
CN_FIRST_NAME.add("初柳");
CN_FIRST_NAME.add("雨南");
CN_FIRST_NAME.add("淑贤");
CN_FIRST_NAME.add("华茂");
CN_FIRST_NAME.add("晴照");
CN_FIRST_NAME.add("元良");
CN_FIRST_NAME.add("思嘉");
CN_FIRST_NAME.add("丽思");
CN_FIRST_NAME.add("雍雅");
CN_FIRST_NAME.add("从云");
CN_FIRST_NAME.add("若翠");
CN_FIRST_NAME.add("雪卉");
CN_FIRST_NAME.add("烨赫");
CN_FIRST_NAME.add("鸿信");
CN_FIRST_NAME.add("小珍");
CN_FIRST_NAME.add("凝远");
CN_FIRST_NAME.add("语柔");
CN_FIRST_NAME.add("文丽");
CN_FIRST_NAME.add("怜阳");
CN_FIRST_NAME.add("乐巧");
CN_FIRST_NAME.add("芷文");
CN_FIRST_NAME.add("振国");
CN_FIRST_NAME.add("半莲");
CN_FIRST_NAME.add("嘉云");
CN_FIRST_NAME.add("俊逸");
CN_FIRST_NAME.add("文乐");
CN_FIRST_NAME.add("修诚");
CN_FIRST_NAME.add("睿慈");
CN_FIRST_NAME.add("丝萝");
CN_FIRST_NAME.add("山柳");
CN_FIRST_NAME.add("音华");
CN_FIRST_NAME.add("亦玉");
CN_FIRST_NAME.add("秀筠");
CN_FIRST_NAME.add("妙思");
CN_FIRST_NAME.add("经纬");
CN_FIRST_NAME.add("骊英");
CN_FIRST_NAME.add("语柳");
CN_FIRST_NAME.add("灵安");
CN_FIRST_NAME.add("端雅");
CN_FIRST_NAME.add("慧丽");
CN_FIRST_NAME.add("夏烟");
CN_FIRST_NAME.add("问凝");
CN_FIRST_NAME.add("水彤");
CN_FIRST_NAME.add("映寒");
CN_FIRST_NAME.add("西华");
CN_FIRST_NAME.add("芳春");
CN_FIRST_NAME.add("雅韵");
CN_FIRST_NAME.add("安萱");
CN_FIRST_NAME.add("友琴");
CN_FIRST_NAME.add("心愫");
CN_FIRST_NAME.add("雅韶");
CN_FIRST_NAME.add("珉瑶");
CN_FIRST_NAME.add("炳君");
CN_FIRST_NAME.add("经纶");
CN_FIRST_NAME.add("欢悦");
CN_FIRST_NAME.add("旎旎");
CN_FIRST_NAME.add("霓云");
CN_FIRST_NAME.add("真洁");
CN_FIRST_NAME.add("俊健");
CN_FIRST_NAME.add("鸣玉");
CN_FIRST_NAME.add("子欣");
CN_FIRST_NAME.add("飞雨");
CN_FIRST_NAME.add("鹏举");
CN_FIRST_NAME.add("元芹");
CN_FIRST_NAME.add("飞雪");
CN_FIRST_NAME.add("华荣");
CN_FIRST_NAME.add("乃心");
CN_FIRST_NAME.add("天路");
CN_FIRST_NAME.add("欣悦");
CN_FIRST_NAME.add("心慈");
CN_FIRST_NAME.add("弘阔");
CN_FIRST_NAME.add("灵寒");
CN_FIRST_NAME.add("修谨");
CN_FIRST_NAME.add("世敏");
CN_FIRST_NAME.add("瑞芝");
CN_FIRST_NAME.add("海颖");
CN_FIRST_NAME.add("温茂");
CN_FIRST_NAME.add("英纵");
CN_FIRST_NAME.add("雨双");
CN_FIRST_NAME.add("雨珍");
CN_FIRST_NAME.add("青曼");
CN_FIRST_NAME.add("盼兰");
CN_FIRST_NAME.add("梓倩");
CN_FIRST_NAME.add("力夫");
CN_FIRST_NAME.add("骊茹");
CN_FIRST_NAME.add("绿夏");
CN_FIRST_NAME.add("锐泽");
CN_FIRST_NAME.add("修永");
CN_FIRST_NAME.add("友瑶");
CN_FIRST_NAME.add("怡嘉");
CN_FIRST_NAME.add("元英");
CN_FIRST_NAME.add("玉山");
CN_FIRST_NAME.add("慧云");
CN_FIRST_NAME.add("古兰");
CN_FIRST_NAME.add("翠巧");
CN_FIRST_NAME.add("韶华");
CN_FIRST_NAME.add("小琴");
CN_FIRST_NAME.add("珑玲");
CN_FIRST_NAME.add("彗云");
CN_FIRST_NAME.add("玄素");
CN_FIRST_NAME.add("晶燕");
CN_FIRST_NAME.add("新觉");
CN_FIRST_NAME.add("月怡");
CN_FIRST_NAME.add("娴淑");
CN_FIRST_NAME.add("霞赩");
CN_FIRST_NAME.add("瑜英");
CN_FIRST_NAME.add("贝莉");
CN_FIRST_NAME.add("国兴");
CN_FIRST_NAME.add("恺歌");
CN_FIRST_NAME.add("素华");
CN_FIRST_NAME.add("小瑜");
CN_FIRST_NAME.add("曜文");
CN_FIRST_NAME.add("浩穰");
CN_FIRST_NAME.add("雯华");
CN_FIRST_NAME.add("碧巧");
CN_FIRST_NAME.add("河灵");
CN_FIRST_NAME.add("娅玟");
CN_FIRST_NAME.add("雪珍");
CN_FIRST_NAME.add("鹏云");
CN_FIRST_NAME.add("雪珊");
CN_FIRST_NAME.add("康成");
CN_FIRST_NAME.add("易巧");
CN_FIRST_NAME.add("艳丽");
CN_FIRST_NAME.add("梦丝");
CN_FIRST_NAME.add("静晨");
CN_FIRST_NAME.add("雁风");
CN_FIRST_NAME.add("山梅");
CN_FIRST_NAME.add("珍瑞");
CN_FIRST_NAME.add("怜雪");
CN_FIRST_NAME.add("思雅");
CN_FIRST_NAME.add("寻雪");
CN_FIRST_NAME.add("端静");
CN_FIRST_NAME.add("志强");
CN_FIRST_NAME.add("语梦");
CN_FIRST_NAME.add("思雁");
CN_FIRST_NAME.add("正奇");
CN_FIRST_NAME.add("夏兰");
CN_FIRST_NAME.add("宾鸿");
CN_FIRST_NAME.add("欣愉");
CN_FIRST_NAME.add("凯乐");
CN_FIRST_NAME.add("文滨");
CN_FIRST_NAME.add("昌黎");
CN_FIRST_NAME.add("俊郎");
CN_FIRST_NAME.add("苒苒");
CN_FIRST_NAME.add("骏英");
CN_FIRST_NAME.add("承泽");
CN_FIRST_NAME.add("笑卉");
CN_FIRST_NAME.add("涵煦");
CN_FIRST_NAME.add("雨琴");
CN_FIRST_NAME.add("采南");
CN_FIRST_NAME.add("嘉佑");
CN_FIRST_NAME.add("思雨");
CN_FIRST_NAME.add("痴凝");
CN_FIRST_NAME.add("梦之");
CN_FIRST_NAME.add("笑南");
CN_FIRST_NAME.add("博艺");
CN_FIRST_NAME.add("愉婉");
CN_FIRST_NAME.add("乐康");
CN_FIRST_NAME.add("正祥");
CN_FIRST_NAME.add("念寒");
CN_FIRST_NAME.add("辰君");
CN_FIRST_NAME.add("自强");
CN_FIRST_NAME.add("沛珊");
CN_FIRST_NAME.add("英彦");
CN_FIRST_NAME.add("依白");
CN_FIRST_NAME.add("青枫");
CN_FIRST_NAME.add("高驰");
CN_FIRST_NAME.add("驰月");
CN_FIRST_NAME.add("文漪");
CN_FIRST_NAME.add("月悦");
CN_FIRST_NAME.add("家美");
CN_FIRST_NAME.add("天亦");
CN_FIRST_NAME.add("谷翠");
CN_FIRST_NAME.add("妙意");
CN_FIRST_NAME.add("冬雁");
CN_FIRST_NAME.add("睿才");
CN_FIRST_NAME.add("弘雅");
CN_FIRST_NAME.add("惠美");
CN_FIRST_NAME.add("梦云");
CN_FIRST_NAME.add("云霞");
CN_FIRST_NAME.add("尔琴");
CN_FIRST_NAME.add("思真");
CN_FIRST_NAME.add("嘉澍");
CN_FIRST_NAME.add("青柏");
CN_FIRST_NAME.add("锦欣");
CN_FIRST_NAME.add("司辰");
CN_FIRST_NAME.add("冬雪");
CN_FIRST_NAME.add("弘益");
CN_FIRST_NAME.add("凡灵");
CN_FIRST_NAME.add("茹雪");
CN_FIRST_NAME.add("弘盛");
CN_FIRST_NAME.add("同济");
CN_FIRST_NAME.add("子民");
CN_FIRST_NAME.add("云露");
CN_FIRST_NAME.add("辰钊");
CN_FIRST_NAME.add("妍芳");
CN_FIRST_NAME.add("文轩");
CN_FIRST_NAME.add("真一");
CN_FIRST_NAME.add("骊萍");
CN_FIRST_NAME.add("静曼");
CN_FIRST_NAME.add("海女");
CN_FIRST_NAME.add("修洁");
CN_FIRST_NAME.add("丰茂");
CN_FIRST_NAME.add("雪瑶");
CN_FIRST_NAME.add("娜兰");
CN_FIRST_NAME.add("永怡");
CN_FIRST_NAME.add("晏静");
CN_FIRST_NAME.add("永思");
CN_FIRST_NAME.add("恨之");
CN_FIRST_NAME.add("姗姗");
CN_FIRST_NAME.add("甘泽");
CN_FIRST_NAME.add("宇文");
CN_FIRST_NAME.add("智刚");
CN_FIRST_NAME.add("弘图");
CN_FIRST_NAME.add("嘉运");
CN_FIRST_NAME.add("惠心");
CN_FIRST_NAME.add("采珊");
CN_FIRST_NAME.add("凝然");
CN_FIRST_NAME.add("奇正");
CN_FIRST_NAME.add("鸿煊");
CN_FIRST_NAME.add("鸿光");
CN_FIRST_NAME.add("修贤");
CN_FIRST_NAME.add("水悦");
CN_FIRST_NAME.add("竹雨");
CN_FIRST_NAME.add("元菱");
CN_FIRST_NAME.add("翠绿");
CN_FIRST_NAME.add("善思");
CN_FIRST_NAME.add("依霜");
CN_FIRST_NAME.add("珺俐");
CN_FIRST_NAME.add("春岚");
CN_FIRST_NAME.add("蓓蕾");
CN_FIRST_NAME.add("伟晔");
CN_FIRST_NAME.add("雯君");
CN_FIRST_NAME.add("恨云");
CN_FIRST_NAME.add("勇锐");
CN_FIRST_NAME.add("慕凝");
CN_FIRST_NAME.add("晨璐");
CN_FIRST_NAME.add("晓霜");
CN_FIRST_NAME.add("鸿熙");
CN_FIRST_NAME.add("靖柏");
CN_FIRST_NAME.add("良俊");
CN_FIRST_NAME.add("靖柔");
CN_FIRST_NAME.add("辰铭");
CN_FIRST_NAME.add("建章");
CN_FIRST_NAME.add("沈雅");
CN_FIRST_NAME.add("南莲");
CN_FIRST_NAME.add("晓露");
CN_FIRST_NAME.add("悠柔");
CN_FIRST_NAME.add("仙仪");
CN_FIRST_NAME.add("海秋");
CN_FIRST_NAME.add("烨伟");
CN_FIRST_NAME.add("千易");
CN_FIRST_NAME.add("可儿");
CN_FIRST_NAME.add("彭泽");
CN_FIRST_NAME.add("英耀");
CN_FIRST_NAME.add("易绿");
CN_FIRST_NAME.add("浩宕");
CN_FIRST_NAME.add("合乐");
CN_FIRST_NAME.add("天佑");
CN_FIRST_NAME.add("晨钰");
CN_FIRST_NAME.add("饮月");
CN_FIRST_NAME.add("问玉");
CN_FIRST_NAME.add("姝好");
CN_FIRST_NAME.add("绮山");
CN_FIRST_NAME.add("慧俊");
CN_FIRST_NAME.add("芳林");
CN_FIRST_NAME.add("玮奇");
CN_FIRST_NAME.add("勇男");
CN_FIRST_NAME.add("品韵");
CN_FIRST_NAME.add("静枫");
CN_FIRST_NAME.add("锦诗");
CN_FIRST_NAME.add("琇云");
CN_FIRST_NAME.add("凝冬");
CN_FIRST_NAME.add("冰真");
CN_FIRST_NAME.add("明德");
CN_FIRST_NAME.add("雅香");
CN_FIRST_NAME.add("自怡");
CN_FIRST_NAME.add("昌翰");
CN_FIRST_NAME.add("秋寒");
CN_FIRST_NAME.add("睿范");
CN_FIRST_NAME.add("骊蓉");
CN_FIRST_NAME.add("和平");
CN_FIRST_NAME.add("从灵");
CN_FIRST_NAME.add("滢渟");
CN_FIRST_NAME.add("景同");
CN_FIRST_NAME.add("鹏运");
CN_FIRST_NAME.add("悦来");
CN_FIRST_NAME.add("凡儿");
CN_FIRST_NAME.add("山槐");
CN_FIRST_NAME.add("兴平");
CN_FIRST_NAME.add("承业");
CN_FIRST_NAME.add("乐心");
CN_FIRST_NAME.add("晗雨");
CN_FIRST_NAME.add("半蕾");
CN_FIRST_NAME.add("辰锟");
CN_FIRST_NAME.add("智勇");
CN_FIRST_NAME.add("滨海");
CN_FIRST_NAME.add("颖慧");
CN_FIRST_NAME.add("紫南");
CN_FIRST_NAME.add("静柏");
CN_FIRST_NAME.add("宏放");
CN_FIRST_NAME.add("红旭");
CN_FIRST_NAME.add("明志");
CN_FIRST_NAME.add("曜曦");
CN_FIRST_NAME.add("青梦");
CN_FIRST_NAME.add("雅秀");
CN_FIRST_NAME.add("如蓉");
CN_FIRST_NAME.add("乐志");
CN_FIRST_NAME.add("闲华");
CN_FIRST_NAME.add("云韶");
CN_FIRST_NAME.add("芷蝶");
CN_FIRST_NAME.add("代丝");
CN_FIRST_NAME.add("言文");
CN_FIRST_NAME.add("兴庆");
CN_FIRST_NAME.add("安易");
CN_FIRST_NAME.add("真仪");
CN_FIRST_NAME.add("君豪");
CN_FIRST_NAME.add("彤云");
CN_FIRST_NAME.add("珠玉");
CN_FIRST_NAME.add("飞飙");
CN_FIRST_NAME.add("宛菡");
CN_FIRST_NAME.add("彭越");
CN_FIRST_NAME.add("紫玉");
CN_FIRST_NAME.add("流惠");
CN_FIRST_NAME.add("安春");
CN_FIRST_NAME.add("俊爽");
CN_FIRST_NAME.add("欣艳");
CN_FIRST_NAME.add("沈靖");
CN_FIRST_NAME.add("建安");
CN_FIRST_NAME.add("奇水");
CN_FIRST_NAME.add("金玉");
CN_FIRST_NAME.add("绿竹");
CN_FIRST_NAME.add("乐怡");
CN_FIRST_NAME.add("怀寒");
CN_FIRST_NAME.add("沈静");
CN_FIRST_NAME.add("英悟");
CN_FIRST_NAME.add("冷雁");
CN_FIRST_NAME.add("高寒");
CN_FIRST_NAME.add("安晏");
CN_FIRST_NAME.add("浓绮");
CN_FIRST_NAME.add("盈秀");
CN_FIRST_NAME.add("瑜蓓");
CN_FIRST_NAME.add("以丹");
CN_FIRST_NAME.add("运凡");
CN_FIRST_NAME.add("傲白");
CN_FIRST_NAME.add("姣妍");
CN_FIRST_NAME.add("修为");
CN_FIRST_NAME.add("运凯");
CN_FIRST_NAME.add("竹韵");
CN_FIRST_NAME.add("俊力");
CN_FIRST_NAME.add("冷雪");
CN_FIRST_NAME.add("醉山");
CN_FIRST_NAME.add("星鹏");
CN_FIRST_NAME.add("雅娴");
CN_FIRST_NAME.add("丽芳");
CN_FIRST_NAME.add("虹玉");
CN_FIRST_NAME.add("力学");
CN_FIRST_NAME.add("菀柳");
CN_FIRST_NAME.add("天逸");
CN_FIRST_NAME.add("囡囡");
CN_FIRST_NAME.add("妙芙");
CN_FIRST_NAME.add("骊文");
CN_FIRST_NAME.add("新语");
CN_FIRST_NAME.add("知睿");
CN_FIRST_NAME.add("景铄");
CN_FIRST_NAME.add("霞辉");
CN_FIRST_NAME.add("宏旷");
CN_FIRST_NAME.add("以云");
CN_FIRST_NAME.add("才哲");
CN_FIRST_NAME.add("华藏");
CN_FIRST_NAME.add("君洁");
CN_FIRST_NAME.add("滢滢");
CN_FIRST_NAME.add("曦晨");
CN_FIRST_NAME.add("冷霜");
CN_FIRST_NAME.add("香芹");
CN_FIRST_NAME.add("南蓉");
CN_FIRST_NAME.add("浩岚");
CN_FIRST_NAME.add("乐悦");
CN_FIRST_NAME.add("星纬");
CN_FIRST_NAME.add("彭丹");
CN_FIRST_NAME.add("云飞");
CN_FIRST_NAME.add("雅媚");
CN_FIRST_NAME.add("姣姣");
CN_FIRST_NAME.add("叶农");
CN_FIRST_NAME.add("菊月");
CN_FIRST_NAME.add("傲雪");
CN_FIRST_NAME.add("温文");
CN_FIRST_NAME.add("怀山");
CN_FIRST_NAME.add("瑜敏");
CN_FIRST_NAME.add("彭湃");
CN_FIRST_NAME.add("紫琼");
CN_FIRST_NAME.add("若芳");
CN_FIRST_NAME.add("又青");
CN_FIRST_NAME.add("心菱");
CN_FIRST_NAME.add("英慧");
CN_FIRST_NAME.add("和美");
CN_FIRST_NAME.add("开宇");
CN_FIRST_NAME.add("辰阳");
CN_FIRST_NAME.add("尔阳");
CN_FIRST_NAME.add("寄翠");
CN_FIRST_NAME.add("从冬");
CN_FIRST_NAME.add("慕卉");
CN_FIRST_NAME.add("念巧");
CN_FIRST_NAME.add("傲霜");
CN_FIRST_NAME.add("曜栋");
CN_FIRST_NAME.add("婉淑");
CN_FIRST_NAME.add("君浩");
CN_FIRST_NAME.add("思天");
CN_FIRST_NAME.add("项明");
CN_FIRST_NAME.add("金鑫");
CN_FIRST_NAME.add("高岑");
CN_FIRST_NAME.add("欣荣");
CN_FIRST_NAME.add("文光");
CN_FIRST_NAME.add("童童");
CN_FIRST_NAME.add("云天");
CN_FIRST_NAME.add("小雨");
CN_FIRST_NAME.add("茂彦");
CN_FIRST_NAME.add("乐意");
CN_FIRST_NAME.add("嘉熙");
CN_FIRST_NAME.add("若英");
CN_FIRST_NAME.add("锐达");
CN_FIRST_NAME.add("和志");
CN_FIRST_NAME.add("华晖");
CN_FIRST_NAME.add("从凝");
CN_FIRST_NAME.add("逸明");
CN_FIRST_NAME.add("鹏煊");
CN_FIRST_NAME.add("兴德");
CN_FIRST_NAME.add("燕珺");
CN_FIRST_NAME.add("小雯");
CN_FIRST_NAME.add("晶瑶");
CN_FIRST_NAME.add("承载");
CN_FIRST_NAME.add("烨烁");
CN_FIRST_NAME.add("婉清");
CN_FIRST_NAME.add("锐进");
CN_FIRST_NAME.add("曲文");
CN_FIRST_NAME.add("依风");
CN_FIRST_NAME.add("白莲");
CN_FIRST_NAME.add("弘壮");
CN_FIRST_NAME.add("刚毅");
CN_FIRST_NAME.add("元旋");
CN_FIRST_NAME.add("子丹");
CN_FIRST_NAME.add("尔白");
CN_FIRST_NAME.add("芊丽");
CN_FIRST_NAME.add("茂德");
CN_FIRST_NAME.add("小霜");
CN_FIRST_NAME.add("海宁");
CN_FIRST_NAME.add("鸿卓");
CN_FIRST_NAME.add("鸿博");
CN_FIRST_NAME.add("韶阳");
CN_FIRST_NAME.add("辰皓");
CN_FIRST_NAME.add("波涛");
CN_FIRST_NAME.add("修伟");
CN_FIRST_NAME.add("贝晨");
CN_FIRST_NAME.add("千柔");
CN_FIRST_NAME.add("逸春");
CN_FIRST_NAME.add("咏德");
CN_FIRST_NAME.add("觅丹");
CN_FIRST_NAME.add("高峯");
CN_FIRST_NAME.add("弘大");
CN_FIRST_NAME.add("歆美");
CN_FIRST_NAME.add("兴怀");
CN_FIRST_NAME.add("水芸");
CN_FIRST_NAME.add("高峰");
CN_FIRST_NAME.add("痴瑶");
CN_FIRST_NAME.add("晟睿");
CN_FIRST_NAME.add("南蕾");
CN_FIRST_NAME.add("烨烨");
CN_FIRST_NAME.add("雨雪");
CN_FIRST_NAME.add("晓夏");
CN_FIRST_NAME.add("访烟");
CN_FIRST_NAME.add("微月");
CN_FIRST_NAME.add("丹萱");
CN_FIRST_NAME.add("千柳");
CN_FIRST_NAME.add("密思");
CN_FIRST_NAME.add("恺乐");
CN_FIRST_NAME.add("阳波");
CN_FIRST_NAME.add("婉丽");
CN_FIRST_NAME.add("和怡");
CN_FIRST_NAME.add("晏如");
CN_FIRST_NAME.add("震博");
CN_FIRST_NAME.add("元明");
CN_FIRST_NAME.add("咏志");
CN_FIRST_NAME.add("兴思");
CN_FIRST_NAME.add("雨真");
CN_FIRST_NAME.add("香莲");
CN_FIRST_NAME.add("以轩");
CN_FIRST_NAME.add("高峻");
CN_FIRST_NAME.add("天元");
CN_FIRST_NAME.add("阳泽");
CN_FIRST_NAME.add("锐逸");
CN_FIRST_NAME.add("尔雅");
CN_FIRST_NAME.add("德明");
CN_FIRST_NAME.add("承运");
CN_FIRST_NAME.add("智鑫");
CN_FIRST_NAME.add("德昌");
CN_FIRST_NAME.add("玉龙");
CN_FIRST_NAME.add("博敏");
CN_FIRST_NAME.add("烨然");
CN_FIRST_NAME.add("职君");
CN_FIRST_NAME.add("飞驰");
CN_FIRST_NAME.add("俊友");
CN_FIRST_NAME.add("晴画");
CN_FIRST_NAME.add("夏瑶");
CN_FIRST_NAME.add("允晨");
CN_FIRST_NAME.add("笑阳");
CN_FIRST_NAME.add("雅宁");
CN_FIRST_NAME.add("俊发");
CN_FIRST_NAME.add("沛白");
CN_FIRST_NAME.add("惜芹");
CN_FIRST_NAME.add("诗丹");
CN_FIRST_NAME.add("夏璇");
CN_FIRST_NAME.add("冰夏");
CN_FIRST_NAME.add("红螺");
CN_FIRST_NAME.add("迎南");
CN_FIRST_NAME.add("白萱");
CN_FIRST_NAME.add("子亦");
CN_FIRST_NAME.add("新洁");
CN_FIRST_NAME.add("学民");
CN_FIRST_NAME.add("沙雨");
CN_FIRST_NAME.add("湛恩");
CN_FIRST_NAME.add("妙菡");
CN_FIRST_NAME.add("宏朗");
CN_FIRST_NAME.add("咏思");
CN_FIRST_NAME.add("运升");
CN_FIRST_NAME.add("博文");
CN_FIRST_NAME.add("香菱");
CN_FIRST_NAME.add("英才");
CN_FIRST_NAME.add("涵瑶");
CN_FIRST_NAME.add("安柏");
CN_FIRST_NAME.add("情文");
CN_FIRST_NAME.add("运华");
CN_FIRST_NAME.add("醉巧");
CN_FIRST_NAME.add("华月");
CN_FIRST_NAME.add("访儿");
CN_FIRST_NAME.add("谷芹");
CN_FIRST_NAME.add("秋巧");
CN_FIRST_NAME.add("雅安");
CN_FIRST_NAME.add("春绿");
CN_FIRST_NAME.add("烨煜");
CN_FIRST_NAME.add("觅云");
CN_FIRST_NAME.add("丝柳");
CN_FIRST_NAME.add("信然");
CN_FIRST_NAME.add("梓玥");
CN_FIRST_NAME.add("尔真");
CN_FIRST_NAME.add("采白");
CN_FIRST_NAME.add("经艺");
CN_FIRST_NAME.add("静槐");
CN_FIRST_NAME.add("雅容");
CN_FIRST_NAME.add("梦兰");
CN_FIRST_NAME.add("君丽");
CN_FIRST_NAME.add("蕴和");
CN_FIRST_NAME.add("淑然");
CN_FIRST_NAME.add("和悌");
CN_FIRST_NAME.add("俊名");
CN_FIRST_NAME.add("琛丽");
CN_FIRST_NAME.add("和悦");
CN_FIRST_NAME.add("思娜");
CN_FIRST_NAME.add("望慕");
CN_FIRST_NAME.add("鹤轩");
CN_FIRST_NAME.add("凝珍");
CN_FIRST_NAME.add("君之");
CN_FIRST_NAME.add("梓珊");
CN_FIRST_NAME.add("刚豪");
CN_FIRST_NAME.add("语诗");
CN_FIRST_NAME.add("曼蔓");
CN_FIRST_NAME.add("暄玲");
CN_FIRST_NAME.add("修远");
CN_FIRST_NAME.add("善芳");
CN_FIRST_NAME.add("夜卉");
CN_FIRST_NAME.add("香萱");
CN_FIRST_NAME.add("夜南");
CN_FIRST_NAME.add("如曼");
CN_FIRST_NAME.add("淑兰");
CN_FIRST_NAME.add("馥芬");
CN_FIRST_NAME.add("玉怡");
CN_FIRST_NAME.add("烨熠");
CN_FIRST_NAME.add("施诗");
CN_FIRST_NAME.add("沛雯");
CN_FIRST_NAME.add("若菱");
CN_FIRST_NAME.add("睿敏");
CN_FIRST_NAME.add("雅寒");
CN_FIRST_NAME.add("秀美");
CN_FIRST_NAME.add("雁山");
CN_FIRST_NAME.add("依秋");
CN_FIRST_NAME.add("彦灵");
CN_FIRST_NAME.add("乐成");
CN_FIRST_NAME.add("婉仪");
CN_FIRST_NAME.add("水荷");
CN_FIRST_NAME.add("泰河");
CN_FIRST_NAME.add("飞章");
CN_FIRST_NAME.add("访冬");
CN_FIRST_NAME.add("冰香");
CN_FIRST_NAME.add("睿文");
CN_FIRST_NAME.add("夜玉");
CN_FIRST_NAME.add("嘉勋");
CN_FIRST_NAME.add("可可");
CN_FIRST_NAME.add("和惬");
CN_FIRST_NAME.add("凯凯");
CN_FIRST_NAME.add("运珊");
CN_FIRST_NAME.add("冠宇");
CN_FIRST_NAME.add("光明");
CN_FIRST_NAME.add("翰翮");
CN_FIRST_NAME.add("笑雯");
CN_FIRST_NAME.add("巧绿");
CN_FIRST_NAME.add("博易");
CN_FIRST_NAME.add("梓琬");
CN_FIRST_NAME.add("南晴");
CN_FIRST_NAME.add("梦凡");
CN_FIRST_NAME.add("代灵");
CN_FIRST_NAME.add("姮娥");
CN_FIRST_NAME.add("凝琴");
CN_FIRST_NAME.add("博明");
CN_FIRST_NAME.add("娅静");
CN_FIRST_NAME.add("凡双");
CN_FIRST_NAME.add("宜春");
CN_FIRST_NAME.add("运珧");
CN_FIRST_NAME.add("曼文");
CN_FIRST_NAME.add("长莹");
CN_FIRST_NAME.add("桂帆");
CN_FIRST_NAME.add("德曜");
CN_FIRST_NAME.add("昊苍");
CN_FIRST_NAME.add("运发");
CN_FIRST_NAME.add("子轩");
CN_FIRST_NAME.add("康时");
CN_FIRST_NAME.add("雨石");
CN_FIRST_NAME.add("毅然");
CN_FIRST_NAME.add("英范");
CN_FIRST_NAME.add("芮欢");
CN_FIRST_NAME.add("芮欣");
CN_FIRST_NAME.add("辰韦");
CN_FIRST_NAME.add("明艳");
CN_FIRST_NAME.add("昊英");
CN_FIRST_NAME.add("理全");
CN_FIRST_NAME.add("刚洁");
CN_FIRST_NAME.add("长菁");
CN_FIRST_NAME.add("振宇");
CN_FIRST_NAME.add("平乐");
CN_FIRST_NAME.add("安梦");
CN_FIRST_NAME.add("立群");
CN_FIRST_NAME.add("如松");
CN_FIRST_NAME.add("运珹");
CN_FIRST_NAME.add("绮彤");
CN_FIRST_NAME.add("浩广");
CN_FIRST_NAME.add("涵畅");
CN_FIRST_NAME.add("忆敏");
CN_FIRST_NAME.add("恬然");
CN_FIRST_NAME.add("又夏");
CN_FIRST_NAME.add("梓瑶");
CN_FIRST_NAME.add("菲菲");
CN_FIRST_NAME.add("梓璐");
CN_FIRST_NAME.add("银瑶");
CN_FIRST_NAME.add("春翠");
CN_FIRST_NAME.add("望舒");
CN_FIRST_NAME.add("德本");
CN_FIRST_NAME.add("思嫒");
CN_FIRST_NAME.add("乐芸");
CN_FIRST_NAME.add("睿明");
CN_FIRST_NAME.add("俊哲");
CN_FIRST_NAME.add("腾逸");
CN_FIRST_NAME.add("子辰");
CN_FIRST_NAME.add("绮美");
CN_FIRST_NAME.add("妍晨");
CN_FIRST_NAME.add("音韵");
CN_FIRST_NAME.add("半梅");
CN_FIRST_NAME.add("佳美");
CN_FIRST_NAME.add("昌茂");
CN_FIRST_NAME.add("飞宇");
CN_FIRST_NAME.add("鸿哲");
CN_FIRST_NAME.add("兴腾");
CN_FIRST_NAME.add("喜悦");
CN_FIRST_NAME.add("问雁");
CN_FIRST_NAME.add("暄和");
CN_FIRST_NAME.add("如柏");
CN_FIRST_NAME.add("斯乔");
CN_FIRST_NAME.add("忆文");
CN_FIRST_NAME.add("谷菱");
CN_FIRST_NAME.add("赞怡");
CN_FIRST_NAME.add("凌雪");
CN_FIRST_NAME.add("子濯");
CN_FIRST_NAME.add("新之");
CN_FIRST_NAME.add("元蝶");
CN_FIRST_NAME.add("泽语");
CN_FIRST_NAME.add("白薇");
CN_FIRST_NAME.add("含海");
CN_FIRST_NAME.add("晓骞");
CN_FIRST_NAME.add("馨荣");
CN_FIRST_NAME.add("乐英");
CN_FIRST_NAME.add("嘉玉");
CN_FIRST_NAME.add("念念");
CN_FIRST_NAME.add("文华");
CN_FIRST_NAME.add("阳云");
CN_FIRST_NAME.add("樱花");
CN_FIRST_NAME.add("承允");
CN_FIRST_NAME.add("苑杰");
CN_FIRST_NAME.add("奇伟");
CN_FIRST_NAME.add("从珊");
CN_FIRST_NAME.add("翠芙");
CN_FIRST_NAME.add("同光");
CN_FIRST_NAME.add("泽民");
CN_FIRST_NAME.add("惜萍");
CN_FIRST_NAME.add("元枫");
CN_FIRST_NAME.add("宛曼");
CN_FIRST_NAME.add("彬炳");
CN_FIRST_NAME.add("野雪");
CN_FIRST_NAME.add("隽巧");
CN_FIRST_NAME.add("彬郁");
CN_FIRST_NAME.add("叶吉");
CN_FIRST_NAME.add("惜萱");
CN_FIRST_NAME.add("柔谨");
CN_FIRST_NAME.add("凌霜");
CN_FIRST_NAME.add("学海");
CN_FIRST_NAME.add("孟乐");
CN_FIRST_NAME.add("又香");
CN_FIRST_NAME.add("绮怀");
CN_FIRST_NAME.add("绮思");
CN_FIRST_NAME.add("依童");
CN_FIRST_NAME.add("丽文");
CN_FIRST_NAME.add("今瑶");
CN_FIRST_NAME.add("三诗");
CN_FIRST_NAME.add("飞尘");
CN_FIRST_NAME.add("雅素");
CN_FIRST_NAME.add("小夏");
CN_FIRST_NAME.add("嘉珍");
CN_FIRST_NAME.add("怀绿");
CN_FIRST_NAME.add("侠骞");
CN_FIRST_NAME.add("智阳");
CN_FIRST_NAME.add("俊喆");
CN_FIRST_NAME.add("鸿畅");
CN_FIRST_NAME.add("秋彤");
CN_FIRST_NAME.add("晴雪");
CN_FIRST_NAME.add("修然");
CN_FIRST_NAME.add("佳思");
CN_FIRST_NAME.add("成弘");
CN_FIRST_NAME.add("珠雨");
CN_FIRST_NAME.add("鸿畴");
CN_FIRST_NAME.add("梅雪");
CN_FIRST_NAME.add("幻丝");
CN_FIRST_NAME.add("锐利");
CN_FIRST_NAME.add("凌青");
CN_FIRST_NAME.add("紫雪");
CN_FIRST_NAME.add("涵阳");
CN_FIRST_NAME.add("琼诗");
CN_FIRST_NAME.add("若蕊");
CN_FIRST_NAME.add("怜容");
CN_FIRST_NAME.add("水蓉");
CN_FIRST_NAME.add("泰清");
CN_FIRST_NAME.add("赞悦");
CN_FIRST_NAME.add("元柳");
CN_FIRST_NAME.add("香薇");
CN_FIRST_NAME.add("松雪");
CN_FIRST_NAME.add("水蓝");
CN_FIRST_NAME.add("艳卉");
CN_FIRST_NAME.add("晴霞");
CN_FIRST_NAME.add("兰芝");
CN_FIRST_NAME.add("松雨");
CN_FIRST_NAME.add("幼丝");
CN_FIRST_NAME.add("运锋");
CN_FIRST_NAME.add("乐荷");
CN_FIRST_NAME.add("思宸");
CN_FIRST_NAME.add("悦欣");
CN_FIRST_NAME.add("尔风");
CN_FIRST_NAME.add("星腾");
CN_FIRST_NAME.add("雪风");
CN_FIRST_NAME.add("白易");
CN_FIRST_NAME.add("语海");
CN_FIRST_NAME.add("会欣");
CN_FIRST_NAME.add("香旋");
CN_FIRST_NAME.add("筠溪");
CN_FIRST_NAME.add("兰芳");
CN_FIRST_NAME.add("盼雁");
CN_FIRST_NAME.add("阳伯");
CN_FIRST_NAME.add("天华");
CN_FIRST_NAME.add("若薇");
CN_FIRST_NAME.add("荷珠");
CN_FIRST_NAME.add("妙旋");
CN_FIRST_NAME.add("翠茵");
CN_FIRST_NAME.add("孤丹");
CN_FIRST_NAME.add("书意");
CN_FIRST_NAME.add("梅青");
CN_FIRST_NAME.add("晓筠");
CN_FIRST_NAME.add("珺琦");
CN_FIRST_NAME.add("莺语");
CN_FIRST_NAME.add("晶霞");
CN_FIRST_NAME.add("梦华");
CN_FIRST_NAME.add("晨风");
CN_FIRST_NAME.add("良吉");
CN_FIRST_NAME.add("奇迈");
CN_FIRST_NAME.add("烨华");
CN_FIRST_NAME.add("忻忻");
CN_FIRST_NAME.add("斯伯");
CN_FIRST_NAME.add("以冬");
CN_FIRST_NAME.add("北辰");
CN_FIRST_NAME.add("文君");
CN_FIRST_NAME.add("令燕");
CN_FIRST_NAME.add("秋翠");
CN_FIRST_NAME.add("芸欣");
CN_FIRST_NAME.add("正平");
CN_FIRST_NAME.add("珺琪");
CN_FIRST_NAME.add("兰若");
CN_FIRST_NAME.add("嘉瑞");
CN_FIRST_NAME.add("闵雨");
CN_FIRST_NAME.add("骏桀");
CN_FIRST_NAME.add("成龙");
CN_FIRST_NAME.add("韵磬");
CN_FIRST_NAME.add("建弼");
CN_FIRST_NAME.add("含之");
CN_FIRST_NAME.add("怡宁");
CN_FIRST_NAME.add("兰英");
CN_FIRST_NAME.add("天玉");
CN_FIRST_NAME.add("淼淼");
CN_FIRST_NAME.add("盼盼");
CN_FIRST_NAME.add("淑华");
CN_FIRST_NAME.add("竹筱");
CN_FIRST_NAME.add("谷蓝");
CN_FIRST_NAME.add("慧君");
CN_FIRST_NAME.add("翠荷");
CN_FIRST_NAME.add("佳悦");
CN_FIRST_NAME.add("茂才");
CN_FIRST_NAME.add("水蕊");
CN_FIRST_NAME.add("虹雨");
CN_FIRST_NAME.add("灵慧");
CN_FIRST_NAME.add("柔洁");
CN_FIRST_NAME.add("泽洋");
CN_FIRST_NAME.add("阳辉");
CN_FIRST_NAME.add("孤云");
CN_FIRST_NAME.add("妙春");
CN_FIRST_NAME.add("秀慧");
CN_FIRST_NAME.add("学义");
CN_FIRST_NAME.add("玉成");
CN_FIRST_NAME.add("梦玉");
CN_FIRST_NAME.add("夏雪");
CN_FIRST_NAME.add("湛芳");
CN_FIRST_NAME.add("闲静");
CN_FIRST_NAME.add("文瑞");
CN_FIRST_NAME.add("香春");
CN_FIRST_NAME.add("语丝");
CN_FIRST_NAME.add("文瑶");
CN_FIRST_NAME.add("初之");
CN_FIRST_NAME.add("佳惠");
CN_FIRST_NAME.add("华楚");
CN_FIRST_NAME.add("书慧");
CN_FIRST_NAME.add("若星");
CN_FIRST_NAME.add("坚诚");
CN_FIRST_NAME.add("含云");
CN_FIRST_NAME.add("半槐");
CN_FIRST_NAME.add("信厚");
CN_FIRST_NAME.add("冰安");
CN_FIRST_NAME.add("愉心");
CN_FIRST_NAME.add("浩思");
CN_FIRST_NAME.add("奇逸");
CN_FIRST_NAME.add("宣朗");
CN_FIRST_NAME.add("惜蕊");
CN_FIRST_NAME.add("谷蕊");
CN_FIRST_NAME.add("芮波");
CN_FIRST_NAME.add("幼仪");
CN_FIRST_NAME.add("听云");
CN_FIRST_NAME.add("妙晴");
CN_FIRST_NAME.add("可嘉");
CN_FIRST_NAME.add("力强");
CN_FIRST_NAME.add("建德");
CN_FIRST_NAME.add("长文");
CN_FIRST_NAME.add("湛英");
CN_FIRST_NAME.add("夏真");
CN_FIRST_NAME.add("敏学");
CN_FIRST_NAME.add("凝阳");
CN_FIRST_NAME.add("忆曼");
CN_FIRST_NAME.add("碧莹");
CN_FIRST_NAME.add("思山");
}
}
|
cod3cat/JavaMasterClass | Constructors/src/com/cod3cat/constructors/VipCustomer.java | <reponame>cod3cat/JavaMasterClass
package com.cod3cat.constructors;
public class VipCustomer {
private String name;
private int creditLimit;
private String customerEMail;
public VipCustomer() {
this("default Name", 25000, "<EMAIL>");
}
public VipCustomer(String name, String customerEMail) {
this(name, 25000, customerEMail);
}
public VipCustomer(String name, int creditLimit, String customerEMail) {
this.name = name;
this.creditLimit = creditLimit;
this.customerEMail = customerEMail;
}
public String getName() {
return name;
}
public int getCreditLimit() {
return creditLimit;
}
public String getCustomerEMail() {
return customerEMail;
}
}
|
shaddyx/LaneJS | lane/js/FormElements/ActionlPanel.js | <filename>lane/js/FormElements/ActionlPanel.js
/**
*
* @constructor
*/
var ActionPanel = function() {
Panel.call(this);
};
Util.extend(ActionPanel, Panel);
ActionPanel.type = "ActionPanel";
|
MattDodsonEnglish/zitadel | internal/project/model/api_config.go | package model
import (
"fmt"
"strings"
"github.com/caos/logging"
"github.com/caos/zitadel/internal/crypto"
"github.com/caos/zitadel/internal/errors"
es_models "github.com/caos/zitadel/internal/eventstore/v1/models"
"github.com/caos/zitadel/internal/id"
)
type APIConfig struct {
es_models.ObjectRoot
AppID string
ClientID string
ClientSecret *crypto.CryptoValue
ClientSecretString string
AuthMethodType APIAuthMethodType
ClientKeys []*ClientKey
}
type APIAuthMethodType int32
const (
APIAuthMethodTypeBasic APIAuthMethodType = iota
APIAuthMethodTypePrivateKeyJWT
)
func (c *APIConfig) IsValid() bool {
return true
}
//ClientID random_number@projectname (eg. 495894098234@zitadel)
func (c *APIConfig) GenerateNewClientID(idGenerator id.Generator, project *Project) error {
rndID, err := idGenerator.Next()
if err != nil {
return err
}
c.ClientID = fmt.Sprintf("%v@%v", rndID, strings.ReplaceAll(strings.ToLower(project.Name), " ", "_"))
return nil
}
func (c *APIConfig) GenerateClientSecretIfNeeded(generator crypto.Generator) (string, error) {
if c.AuthMethodType == APIAuthMethodTypeBasic {
return c.GenerateNewClientSecret(generator)
}
return "", nil
}
func (c *APIConfig) GenerateNewClientSecret(generator crypto.Generator) (string, error) {
cryptoValue, stringSecret, err := crypto.NewCode(generator)
if err != nil {
logging.Log("MODEL-ADvd2").OnError(err).Error("unable to create client secret")
return "", errors.ThrowInternal(err, "MODEL-dsvr43", "Errors.Project.CouldNotGenerateClientSecret")
}
c.ClientSecret = cryptoValue
return stringSecret, nil
}
|
meghana-rajashekar/testing-intersight | apis/workflow/v1alpha1/zz_generated.managedlist.go | /*
Copyright 2021 The Crossplane Authors.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
// Code generated by angryjet. DO NOT EDIT.
package v1alpha1
import resource "github.com/crossplane/crossplane-runtime/pkg/resource"
// GetItems of this AnsibleBatchExecutorList.
func (l *AnsibleBatchExecutorList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this BatchApiExecutorList.
func (l *BatchApiExecutorList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this CustomDataTypeDefinitionList.
func (l *CustomDataTypeDefinitionList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this ErrorResponseHandlerList.
func (l *ErrorResponseHandlerList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this RollbackWorkflowList.
func (l *RollbackWorkflowList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this SolutionActionDefinitionList.
func (l *SolutionActionDefinitionList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this SolutionActionInstanceList.
func (l *SolutionActionInstanceList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this SolutionDefinitionList.
func (l *SolutionDefinitionList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this SolutionInstanceList.
func (l *SolutionInstanceList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this SolutionOutputList.
func (l *SolutionOutputList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this SshBatchExecutorList.
func (l *SshBatchExecutorList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this TaskDefinitionList.
func (l *TaskDefinitionList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this WorkflowDefinitionList.
func (l *WorkflowDefinitionList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
// GetItems of this WorkflowInfoList.
func (l *WorkflowInfoList) GetItems() []resource.Managed {
items := make([]resource.Managed, len(l.Items))
for i := range l.Items {
items[i] = &l.Items[i]
}
return items
}
|
wesleyendliche/Python_exercises | World_1/018sincostan.py | <gh_stars>0
from math import radians, sin, cos, tan
an = float(input('Digite o ângulo que você deseja: '))
seno = sin(radians(an))
print('O ângulo de {} tem o SENO de {:.2f}'.format(an, seno))
cosseno = cos(radians(an))
print('O ângulo de {} tem o COSSENO de {:.2f}'.format(an, cosseno))
tangente = tan(radians(an))
print('O ângulo de {} tem a TANGENTE de {:.2f}'.format(an, tangente))
|
iamjli/pyranges | tests/test_pickle.py | <filename>tests/test_pickle.py
import pyranges as pr
import pickle
def test_pickle():
gr = pr.data.f1()
pickle.dump(gr, open("hi", "wb+"))
gr2 = pickle.load(open("hi", "rb"))
|
homich1991/ignite | modules/core/src/test/java/org/apache/ignite/internal/processors/service/IgniteServiceReassignmentTest.java | <gh_stars>1-10
/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.ignite.internal.processors.service;
import java.util.concurrent.ThreadLocalRandom;
import org.apache.ignite.Ignite;
import org.apache.ignite.IgniteException;
import org.apache.ignite.configuration.IgniteConfiguration;
import org.apache.ignite.internal.util.typedef.PA;
import org.apache.ignite.resources.IgniteInstanceResource;
import org.apache.ignite.services.Service;
import org.apache.ignite.services.ServiceConfiguration;
import org.apache.ignite.services.ServiceContext;
import org.apache.ignite.spi.discovery.tcp.TcpDiscoverySpi;
import org.apache.ignite.spi.discovery.tcp.ipfinder.TcpDiscoveryIpFinder;
import org.apache.ignite.spi.discovery.tcp.ipfinder.vm.TcpDiscoveryVmIpFinder;
import org.apache.ignite.testframework.GridTestUtils;
import org.apache.ignite.testframework.junits.common.GridCommonAbstractTest;
/**
*
*/
public class IgniteServiceReassignmentTest extends GridCommonAbstractTest {
/** */
private static final TcpDiscoveryIpFinder IP_FINDER = new TcpDiscoveryVmIpFinder(true);
/** */
private ServiceConfiguration srvcCfg;
/** {@inheritDoc} */
@Override protected IgniteConfiguration getConfiguration(String igniteInstanceName) throws Exception {
IgniteConfiguration cfg = super.getConfiguration(igniteInstanceName);
((TcpDiscoverySpi)cfg.getDiscoverySpi()).setIpFinder(IP_FINDER);
if (srvcCfg != null)
cfg.setServiceConfiguration(srvcCfg);
return cfg;
}
/** {@inheritDoc} */
@Override protected void afterTest() throws Exception {
stopAllGrids();
super.afterTest();
}
/**
* @throws Exception If failed.
*/
public void testNodeRestart1() throws Exception {
srvcCfg = serviceConfiguration();
Ignite node1 = startGrid(1);
assertEquals(42, serviceProxy(node1).foo());
srvcCfg = serviceConfiguration();
Ignite node2 = startGrid(2);
node1.close();
waitForService(node2);
assertEquals(42, serviceProxy(node2).foo());
srvcCfg = serviceConfiguration();
Ignite node3 = startGrid(3);
assertEquals(42, serviceProxy(node3).foo());
srvcCfg = serviceConfiguration();
node1 = startGrid(1);
assertEquals(42, serviceProxy(node1).foo());
assertEquals(42, serviceProxy(node2).foo());
assertEquals(42, serviceProxy(node3).foo());
node2.close();
waitForService(node1);
assertEquals(42, serviceProxy(node1).foo());
assertEquals(42, serviceProxy(node3).foo());
}
/**
* @throws Exception If failed.
*/
public void testNodeRestart2() throws Exception {
startGrids(3);
ServiceConfiguration svcCfg = new ServiceConfiguration();
svcCfg.setName("DummyService");
svcCfg.setTotalCount(10);
svcCfg.setMaxPerNodeCount(1);
svcCfg.setService(new DummyService());
ignite(0).services().deploy(svcCfg);
for (int i = 0; i < 3; i++)
assertEquals(42, serviceProxy(ignite(i)).foo());
for (int i = 0; i < 3; i++)
startGrid(i + 3);
for (int i = 0; i < 3; i++)
stopGrid(i);
for (int i = 0; i < 3; i++)
assertEquals(42, serviceProxy(ignite(i + 3)).foo());
}
/**
* @throws Exception If failed.
*/
public void testNodeRestartRandom() throws Exception {
final int NODES = 5;
Ignite ignite = startGridsMultiThreaded(NODES);
ignite.services().deploy(serviceConfiguration());
for (int i = 0; i < 30; i++) {
log.info("Iteration: " + i);
int stopIdx = ThreadLocalRandom.current().nextInt(NODES);
stopGrid(stopIdx);
for (int nodeIdx = 0; nodeIdx < NODES; nodeIdx++) {
if (nodeIdx == stopIdx)
continue;
waitForService(ignite(nodeIdx));
assertEquals(42, serviceProxy(ignite(nodeIdx)).foo());
}
startGrid(stopIdx);
for (int nodeIdx = 0; nodeIdx < NODES; nodeIdx++)
assertEquals(42, serviceProxy(ignite(nodeIdx)).foo());
}
}
/**
* @param node Node.
* @throws Exception If failed.
*/
private void waitForService(final Ignite node) throws Exception {
assertTrue(GridTestUtils.waitForCondition(new PA() {
@Override public boolean apply() {
try {
serviceProxy(node).foo();
return true;
}
catch (IgniteException ignored) {
return false;
}
}
}, 5000));
}
/**
* @param node Node.
* @return Service proxy.
*/
private static MyService serviceProxy(Ignite node) {
return node.services().serviceProxy("DummyService", MyService.class, true);
}
/**
* @return Service configuration.
*/
private ServiceConfiguration serviceConfiguration() {
ServiceConfiguration svc = new ServiceConfiguration();
svc.setName("DummyService");
svc.setTotalCount(1);
svc.setService(new DummyService());
return svc;
}
/**
*
*/
public interface MyService {
/**
* @return Dummy result.
*/
int foo();
}
/**
*
*/
static class DummyService implements MyService, Service {
/** */
@IgniteInstanceResource
private Ignite locNode;
/** {@inheritDoc} */
@Override public void cancel(ServiceContext ctx) {
locNode.log().info("Service cancelled [execId=" + ctx.executionId() +
", node=" + locNode.cluster().localNode() + ']');
}
/** {@inheritDoc} */
@Override public void init(ServiceContext ctx) {
locNode.log().info("Service initialized [execId=" + ctx.executionId() +
", node=" + locNode.cluster().localNode() + ']');
}
/** {@inheritDoc} */
@Override public void execute(ServiceContext ctx) {
locNode.log().info("Service started [execId=" + ctx.executionId() +
", node=" + locNode.cluster().localNode() + ']');
}
/** {@inheritDoc} */
@Override public int foo() {
locNode.log().info("Service called.");
return 42;
}
}
}
|
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