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coverage: 43.416% (+0.1%) from 43.316%
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v1.8.5: Ingest Stražar 2023 HLA-II mono-allelic (PMID 37301199) (#62)

* v1.8.5: Ingest Stražar 2023 HLA-II mono-allelic (PMID 37301199)

Adds Stražar et al. 2023 (Immunity) as supplementary HLA-II data via the
paper's mmc3.zip (Table S2 / ST_ligands_merged.csv), filtered to the
current-study subset (dataset == internal_aff_clean1and2) to avoid
duplicating public rows already present in IEDB and Abelin 2019.

- 308,418 peptide-allele pairs across 42 mono-allelic HLA-II heterodimers
  (20 DQ, 13 DP, 9 DR) profiled in Expi293F cells with HLA-DM co-expression
  and Strep-tag II / Strep-Tactin XT purification
- PMID override records study metadata, per-allele sample panel, and a
  mono_allelic_method ("Strep-tag II") that flags resolved DQ/DP/DR pairs
  as mono-allelic without a cell-line host
- classify_allele_resolution() now recognizes paired class II strings
  (HLA-DQA1*01:03/DQB1*06:03, HLA-DPA1*02:01/DPB1*05:01) as resolved,
  fixing a gate that previously blocked mono_allelic_method overrides
- Tests cover paired allele resolution, Stražar method-based mono-allelic
  classification, supplementary load counts, and exported sample metadata

* Stražar 2023: drop redundant cell_line override, use Pair isinstance

- Remove `override: cell_line` from the Stražar PMID entry. With
  culture_condition="Cell Line / Clone" and cell_name="Expi293F", the
  default classification already yields is_cancer=True for these rows,
  so the explicit override was a no-op. Leaving it empty matches the
  Abelin 2019 MAPTAC convention (PMID 31495665) for tagged-allele
  mono-allelic studies.
- In classify_allele_resolution, replace the stringly-typed
  `type(result).__name__ == "Pair"` check with proper
  `isinstance(result, Pair)` using mhcgnomes.pair.Pair, and read
  resolution from alpha.allele_fields / beta.allele_fields rather than
  re-parsing the serialized form.

* Vectorize scan_supplementary — 4.9x faster on 434k rows

Ingesting Stražar 2023 grew the supplementar... (continued)

1210 of 2787 relevant lines covered (43.42%)

0.43 hits per line

Coverage Regressions

Lines Coverage ∆ File
32
82.53
 -1.1% curation.py
6
86.36
 -3.29% supplement.py
Jobs
ID Job ID Ran Files Coverage
1 24561640591.1 19
43.42
 GitHub Action Run
Source Files on build 24561640591