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Make native mutation datasets portable with verified references - #573
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Native mutation archives currently reopen the original annotation database while restoring supporting transcripts, so moving a result or deleting its temporary reference can prevent scoring and construct replay. This change restores transcript metadata lazily using released PyEnsembl 2.22.2 and exports custom-reference resources into a verified, relative sibling bundle.
Loading verifies size/SHA-256, preserves the exact reference/gene/transcript identity, and never substitutes an old path or another release. Missing resources still allow retained evidence and construct replay; annotation indexing is an explicit local-only operation. Saved protein IDs avoid annotation lookups during construct replay, including legacy archives with matching recorded transcript provenance. Evidence-only re-save retains the expected resource checksums.
Standard Ensembl release/species identity remains intact, with explicitly attached local DNA bundled. Move the native CSV/TSV and its
.referencesdirectory together for annotation work; bundle size reflects the custom reference resources supplied.Validation: lint passes; 24 focused regressions pass, including both BAM strands, fresh-process relocation, actual annotation/effect queries, legacy archives, missing/tampered resources, attached reference DNA, and CLI peptide/mRNA FASTA plus PDF output. The final full suite passes: 2,135 tests, with the existing 38 expected warnings.
Closes #563. Upstream lazy locus restoration shipped in openvax/pyensembl#436 (fixes openvax/pyensembl#435), published as 2.22.2. Vaxrank version: 3.37.2.