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mikessh commited on
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prebuilt caches: whole-proteome window indexes and mimicry reference indexes

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Every one of these is a pure function of data already in this dataset, and each was rebuilt inside
every process that needed it because the in-memory caches are per process. Measured on Aldan-3
2026-09-03 in a Nextflow fan-out, all four tasks missing at once: ~194 s per mimicry task.

proteome_index/<key>.{idx,meta.npz} human + mouse, L=8..11 (the class-I ladder), 17 GB
mimicry_refs/<key>/ mhc1 human + mouse, 24 seqtree indexes each, 1.9 GB

Build vs load, measured: human index L=9 64.6 s -> 0.7 s; mimicry refs human 65.3 s -> 0.4 s.

<key> is a blake2b digest of the content the entry is derived from -- for an index, every protein
name and sequence in iteration order plus the window length -- so the name a publisher computes and
the name a reader computes agree without either being told which proteome it is, and an entry
cannot outlive what produced it. mhcmatch fetches these through `bootstrap --index`; a miss falls
through to building locally, so nothing here is required.

This view is limited to 50 files because it contains too many changes.   See raw diff
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