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pirl-unc / tsarina / 27041807643
71%

Build:
DEFAULT BRANCH: main
Ran 05 Jun 2026 09:47PM UTC
Jobs 1
Files 35
Run time 1min
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05 Jun 2026 09:46PM UTC coverage: 71.313% (+0.04%) from 71.276%
27041807643

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Add `tsarina hits --healthy-tissue` per-peptide safety screen (#91)

Surfaces the #76 cta_healthy_tissue_ms_hits helper in the CLI (it was
Python-API-only). The flag short-circuits `tsarina hits` to output the gene's
per-peptide healthy-SOMATIC-tissue MS hits — tissue, allele, allele_set,
provenance, pmid, and a vital_organ flag (against SAFETY_TISSUE_GROUPS) —
instead of the cancer-MS aggregation. Reproductive/thymic hits (expected for
CTAs) are excluded.

Reproduces the issue's deep-dive from the CLI:
  tsarina hits --gene MAGEA4 --healthy-tissue  -> 3 heart hits (vital_organ=True)
  tsarina hits --gene PRAME  --healthy-tissue  -> 1 clean blood hit

Tests for the flag + no-hits case; existing handle() Namespace builders updated
with the new field. Docs updated. Version 1.4.9 -> 1.5.0.

2471 of 3465 relevant lines covered (71.31%)

0.71 hits per line

Coverage Regressions

Lines Coverage ∆ File
61
56.85
1.05% cli_hits.py
Jobs
ID Job ID Ran Files Coverage
1 27041807643.1 05 Jun 2026 09:47PM UTC 35
71.31
GitHub Action Run
Source Files on build 27041807643
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  • Coverage Changed 1
Coverage ∆ File Lines Relevant Covered Missed Hits/Line
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