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Ran 04 Jun 2026 10:54PM UTC

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Committed 04 Jun 2026 10:53PM UTC coverage: 71.234% (+0.1%) from 71.104%

Job # 26984410485.1

Build Type

push

github

Committed by

web-flow

Commit Message

Document CTA evidence tiers + add cta_healthy_tissue_ms_hits helper (#76) (#88)

Two doc/API gaps that made it hard for consumers (e.g. vaxrank) to sanity-check
CTA tiers and understand what drives a cautious tier.

- docs/curation.md: add a "published CTAs across the axes" reference table
  (NY-ESO-1, NUTM1, HORMAD1, PAGE2/5, MAGE-A4, PRAME, XAGE1A), spell out the
  restriction_confidence formula (>=1.2 HIGH, >=0.8 MODERATE, else LOW), and
  state the teaching point: tiers describe evidence *quality*, not target
  *validity* — a hard TESTIS/PLACENTAL x >=MODERATE gate would reject
  MAGE-A4 (FDA-approved), PRAME, and XAGE1A. Use tiers as ranking signals.

- cta_healthy_tissue_ms_hits(gene): surface healthy-*somatic*-tissue MS hits at
  peptide x tissue x allele granularity (allele set, provenance, PMID, and a
  vital-organ flag against SAFETY_TISSUE_GROUPS). Reproduces the issue's
  deep-dive exactly: PRAME = 1 clean blood hit; MAGE-A4 = 3 heart-eluted
  peptides (HLA-B*49:01, PMID 33858848) + 1 blood. Exported + mocked tests.

Version 1.4.6 -> 1.4.7.

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2459 of 3452 relevant lines covered (71.23%)

0.71 hits per line

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