pirl-unc / tsarina

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• add-filtered-alias
• add-mageb6-cta-79
• add-real-hitlist-integration-test
• add-refs-format-20260420
• add-xage2-lower-cta-thresholds
• address-69-memory-hotpaths
• audit-hitlist-tsa-goal-20260420
• backfill-aliases-resolution-77
• bump-hitlist-pin-1.30.49
• bump-hitlist-pin-1.30.57
• cache-kmer-enumeration-20260420
• close-tsarina-4-via-load-all-evidence
• codex/ctag-display-label
• codex/fix-xage-ms-counts
• codex/live-hitlist-ms-panel
• codex/mhcflurry-full-batch-progress
• consolidate-iedb-drop-netmhcpan-shim
• cta-exclusive-ms-counts
• cta-passes-filters-threshold-098
• deconvolve-multiallelic-ms-evidence
• delegate-to-hitlist-proteome-kmer-set-20260422
• docs/hitlist-data-and-viral-defaults
• document-evidence-tiers-ms-helper-76
• document-scope-provenance-79
• drop-local-aggregate-refs-20260420
• feature/panel-cta-safety-and-nyeso-group
• feature/panel-ms-evidence-tiers
• feature/panel-progress-summary-table
• feature/panel-version-peptide-progress
• feature/spanning-alias-help-smoke-tests
• fix-gene-name-docstring
• fix-mhcflurry-c1505-speed
• fix-test-suite-oom-mhcflurry-stub
• fix/curation-audit-fixes
• fix/ms-evidence-normalization
• fix/panel-healthy-ms-gene-veto
• fix/panel-ms-metrics
• fix/panel-vital-ntpm-threshold
• group-identical-cta-peptide-panels
• group-identical-cta-peptide-sets
• handle-peptide-attribution-provenance
• hitlist-1.15-pin-and-length-pushdown
• hitlist-1.6.0-integration
• main
• ms-curation
• panel-mage-safety-summary-sort
• perf/memory-aware-test-workers
• refs-and-cache-integration-tests-20260421
• simplify-species-kwargs-for-hitlist-1.9
• sort-cta-coverage-first
• spanning-pmhc-set-20260420
• spanning-progress-20260421
• spanning-test-polish-20260421
• tcga-prevalence-evidence-and-summary
• unify-kmer-enumeration-20260421
• untrack-uv-lock
• warn-binding-assays-on-cached-path
• wire-alias-resolution-selection-77
• xage1-aliases-group-77

Build # 26993966076

Build Type

push

github

Committed by web-flow

Commit Message

Document CTA scope (protein-coding only) + source provenance (closes #79) (#90)

Resolves the two remaining #79 items, both already decided by existing design:

- lncRNA/antisense scope: tsarina is protein-coding only (the biotype filter
  rejects non-coding genes), so CTexploreR's lncRNA/antisense CT genes are
  deliberately out of scope.
- Provenance: source_databases is populated for every gene (no sourceless /
  literature-only entries — verified all 360 carry >=1 published-source token).
  Curated CT database (CTpedia/CTexploreR, 285 genes) vs screen-only
  (daSilva2017, 75) is queryable directly; documented with a filtering recipe.

The #79 "143 HPA/literature-only genes" figure came from a stale pirlygenes
bundled snapshot; current tsarina has 0 sourceless genes.

Version 1.4.8 -> 1.4.9.

Coverage Stats

2464 of 3457 relevant lines covered (71.28%)

0.71 hits per line