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main: 82%

Ran 03 Jun 2026 01:15AM UTC

Files 35

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Committed 03 Jun 2026 01:12AM UTC coverage: 80.695% (-0.1%) from 80.811%

Job # 26857655499.4

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 10008 relevant lines covered (80.7%)

0.81 hits per line

pirl-unc / tcrsift / 26857655499 / 4
82%
main: 82%

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Source Files on job python-3.12 - 26857655499.4

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82%
main: 82%

README BADGES
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