25831129826
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Ran 13 May 2026 11:00PM UTC

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Build # 25831129826

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push

github

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web-flow

Commit Message

Fix LENS / pVACseq path: populate per_allele_scores at load time (#294)

The 3.1.0 single-mechanism refactor (#291) moved per-(peptide, allele)
scoring to the DSL and stored the result on
``CandidateEpitope.per_allele_scores``. ``predict_epitopes`` was
updated to populate it; the external-input loaders (``load_lens`` /
``load_pvacseq``) were not.

Result: every external-loaded epitope had ``epitope_score == 0``, so
``target_epitope_score`` was 0, ``combined_score`` collapsed to 0,
and ranking dropped every variant as "No epitopes for peptide." End
users running ``vaxrank --input-pvacseq`` or ``--input-lens`` got
empty reports.

Caught with a real-world smoke against cAIrn's HCC1395 pVACseq TSV
(317 rows in, 0 variants ranked before the fix; 23 ranked after).

Fix: add ``attach_per_allele_scores(epitopes, cfg=None)`` to
``epitope_dsl`` — runs the same DSL pipeline the upstream path uses,
on the loaded epitopes, and stamps each one's per_allele_scores.
Call it at the end of both loaders. Default ``EpitopeConfig()`` so
the loader path's default scoring matches pre-3.1 semantics
exactly. Two regression tests pin both loaders.

832 tests pass, lint clean.

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