pirl-unc / tcrsift / 25818564171
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coverage: 71.229% (+0.2%) from 70.998%
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Structured public-DB annotation columns + match_strictness (#48 phase A) (#52)

* Structured public-DB annotation columns + match_strictness (#48 phase A)

Phase A of #48 — propagate the structured fields already present in
the loaders, add a coarse category classifier, and replace the
implicit β-only fallback with an explicit knob.

New columns emitted by match_clonotypes:

- db_protein — most common antigen_gene per match (e.g. "pp65",
  "MLANA", "EBNA-3"). Lets callers ask "how many of my top clones
  are MART-1" at protein granularity instead of just species.
- db_mhc — most common MHC allele per match. Already present in
  loader output for VDJdb and (after #49) IEDB; just not propagated.
- db_category — viral / bacterial / self / tumor_self / other /
  unknown. Tumor-associated self antigens (MART-1, NY-ESO-1, MAGE-A*,
  gp100, tyrosinase, CEA, WT1, telomerase, HER2, ...) override the
  species-derived bucket so they don't appear as plain "self". The
  override is independent of species: a curated antigen name wins
  over the source organism.
- db_match_strength — "ab" or "b_only". Avoids forcing downstream
  code to special-case db_match_partial.

New match_clonotypes parameter `match_strictness`:

- "strict_ab" — αβ only, no β-only fallback. Use when you want
  headline match counts you can trust.
- "ab_with_partial" — αβ first, β-only fallback per clone. Same
  semantics as legacy match_by="CDR3ab", which remains the default.
- "b_only" — β-only. Same as legacy match_by="CDR3b_only".

Legacy match_by parameter still works; match_strictness takes
precedence when both are set.

The new columns are also added to annotate_clonotypes' no-database
short-circuit so downstream code can rely on the column set being
stable regardless of whether annotation actually ran.

Bumps to 0.8.11. Plots (phase B per the issue) follow separately.

Refs #48.

* Address self-review on #48 phase A

- TUMOR_SELF_ANTIGEN_PATTERNS: switch substring matching to
  word-bo... (continued)

4736 of 6649 relevant lines covered (71.23%)

2.85 hits per line

Coverage Regressions

Lines Coverage ∆ File
10
96.11
 1.01% annotate.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.10 - 25818564171.1 25
71.22
 GitHub Action Run
2 python-3.12 - 25818564171.2 25
71.22
 GitHub Action Run
3 python-3.11 - 25818564171.3 25
71.22
 GitHub Action Run
4 python-3.9 - 25818564171.4 25
71.19
 GitHub Action Run
Source Files on build 25818564171