openvax / topiary / 24490513784

88%

master: 90%

Build Type

Pull #138

github

Committed by iskandr

Commit Message

Add 1aa indel candidate matching to SelfProteome.nearest

When include_indels=True (default), after the same-length SIMD scan
finds a best substitution match, the method also checks whether any
1-deletion (L-1) or 1-insertion (L+1) neighbor of the query exists
in the reference.  An indel match at edit_distance=1 beats a
same-length match at edit_distance≥2.

Cost: ~L + L×20 ≈ 200 hash-set lookups per query (for 9-mers).
The indel check only fires when the same-length best has
edit_distance ≥ 2 — exact matches and 1-substitution matches short-
circuit.  Reference peptide sets at each length are built lazily on
first use and cached.

New output column: self_nearest_edit_type ("deletion" / "insertion")
on indel-matched rows.  Same-length matches don't set this column.

4 new tests: deletion beats distant substitution, insertion match
found at L+1, exact match beats indel, include_indels=False disables.

38 self_proteome tests pass (up from 34).  Full suite 1179 pass
(up from 1170).  Lint clean.

Pull Request Pull Request #138: SelfProteome: include= rename, protected_tissues, BLOSUM62, indels (part B of #124)

Coverage Stats

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

11 existing lines in 1 file now uncovered.

3689 of 4173 relevant lines covered (88.4%)

2.65 hits per line