openvax / topiary / 24516756536

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SelfProteome: include= rename, protected_tissues, BLOSUM62, indels — v5.9.0 (#138)

Part B of #124.  Four additions to SelfProteome:

1. Rename scope= → include= (reads naturally at call site).
2. include="protected_tissues" — multi-species safe (pirlygenes/HPA
   for human, tissue_gene_ids= for any species).
3. BLOSUM62 distance metric (default, lazy Biopython load).
   Conservative subs get lower distances than non-conservative.
4. 1aa indel candidates (deletion + insertion at L±1 via hash-set
   lookup, ~200 checks per 9-mer).

39 self_proteome tests.  1180 total passing.

109 of 112 new or added lines in 1 file covered. (97.32%)

3689 of 4173 relevant lines covered (88.4%)

2.65 hits per line