23872660807
80%

Ran 01 Apr 2026 09:52PM UTC

Jobs 1

Files 11

Run time 1min

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Committed 01 Apr 2026 09:52PM UTC coverage: 35.86% (+4.3%) from 31.535%

Build # 23872660807

Build Type

push

github

Committed by

web-flow

Commit Message

Add mono-allelic sample detection for allele assignment confidence (#1)

* Split CLAUDE.md into AGENTS.md + slim CLAUDE.md for Codex+Claude compatibility

AGENTS.md contains shared instructions (verification, workflow, principles)
that both Codex and Claude Code follow. CLAUDE.md references it and adds
Claude Code-specific plan mode and subagent strategy.

* Add mono-allelic sample detection for allele assignment confidence

Detect known HLA-null/low cell line hosts (721.221, C1R, K562, T2) and
flag pMHC observations from these systems as mono-allelic — meaning the
peptide-allele assignment is unambiguous. C1R's endogenous HLA-B*35:03
and HLA-C*04:01 are tracked to avoid false confidence.

New columns propagate through aggregation (has_mono_allelic_evidence,
ms_pmhc_has_mono_evidence) so downstream consumers like tsarina can
weight mono-allelic evidence higher during scoring.

* Fix lint: prefix unused host vars with underscore

Coverage Stats

317 of 884 relevant lines covered (35.86%)

0.36 hits per line

Coverage Regressions

Lines	Coverage	∆	File
49	0.0	0.0%	report.py
13	87.74	2.85%	curation.py
3	87.1	0.43%	samples.py
1	23.81	0.0%	scanner.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	23872660807.1	01 Apr 2026 09:52PM UTC	11	35.86	GitHub Action Run

pirl-unc / hitlist / 23872660807
80%

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Coverage Regressions

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Source Files on build 23872660807

pirl-unc / hitlist / 23872660807 80%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

Coverage Regressions

Jobs

Source Files on build 23872660807

pirl-unc / hitlist / 23872660807
80%

README BADGES
x