26857655499
82%

Ran 03 Jun 2026 01:14AM UTC

Jobs 4

Files 35

Run time 1min

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Committed 03 Jun 2026 01:12AM UTC coverage: 80.704% (-0.1%) from 80.82%

Build # 26857655499

Build Type

push

github

Committed by

web-flow

Commit Message

Map unsupported/novel V/J alleles to nearest supported before Pgen/Ppost (#150) (#154)

Removes the silent default-usage-mask fallback for alleles OLGA/SONIA
don't recognize — an unrecognized CellRanger call or a novel allele from
the audit. Such alleles previously gave a degraded Q/Ppost (or NaN); now
they are mapped to the nearest supported allele BEFORE scoring, and every
substitution is logged.

- nearest_supported_allele(gene, chain, segment) + the pure, fully-tested
  _nearest_in_supported(gene, supported) with tiered mapping:
  exact -> nearest_allele (same gene, lowest supported allele) ->
  nearest_gene (closest gene by locus/family/subgroup name distance, *01)
  -> unmapped.
- compute_pgen_ppost gains map_unsupported=True + optional used_v_col/
  used_j_col to record the allele actually used; logs original->sub+reason.
- annotate_nearest_supported_allele(df, chain, segment, gene_col) so a
  detected novel allele carries its downstream substitution auditably.
- Pure mapping tests (no model) + model-backed substitution test. Docs.

Bump 2.23.0.

Coverage Stats

8076 of 10007 relevant lines covered (80.7%)

3.23 hits per line

Coverage Regressions

Lines	Coverage	∆	File
91	50.92	7.56%	olga_ppost.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.11 - 26857655499.1	03 Jun 2026 01:14AM UTC	35	80.7	GitHub Action Run
2	python-3.9 - 26857655499.2	03 Jun 2026 01:14AM UTC	35	80.65	GitHub Action Run
3	python-3.10 - 26857655499.3	03 Jun 2026 01:14AM UTC	35	80.7	GitHub Action Run
4	python-3.12 - 26857655499.4	03 Jun 2026 01:15AM UTC	35	80.7	GitHub Action Run

pirl-unc / tcrsift / 26857655499
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pirl-unc / tcrsift / 26857655499 82%

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