26971037794
71%

Ran 04 Jun 2026 06:21PM UTC

Jobs 1

Files 35

Run time 1min

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Committed 04 Jun 2026 06:20PM UTC coverage: 70.824% (+0.03%) from 70.796%

Build # 26971037794

Build Type

push

github

Committed by

web-flow

Commit Message

Add XAGE2, lower no-protein CTA gate to 0.97, parameterize floor + rescue XAGE5 (#80)

Surfaces the XAGE-family CTAs requested, after investigating each gene's
actual HPA evidence.

- Add XAGE2 (ENSG00000155622, CTpedia/CT12.2; closes part of #79). Row built
  from HPA rna_tissue_consensus.tsv via the in-repo generators
  (tiers.enrich_rna_per_tissue + assign_all_axes); reproducible via
  scripts/add_xage2.py. XAGE2 has real lung expression (5.3 nTPM, replicates
  across GTEx/HPA/FANTOM -- not contamination), so it carries safety_flags=lung.

- Lower the no-protein/Uncertain adaptive reproductive-fraction gate 0.98 -> 0.97
  (HPA_ADAPTIVE_PROTEIN_RNA_THRESHOLDS). Admits XAGE2 (0.977) plus CT83/KK-LC-1
  (0.975) and PRM3 (0.979); DPPA3 (0.969) stays out.

- Parameterize the never_expressed floor as HPA_EXPRESSION_FLOOR_NTPM = 2.0 and
  rescue borderline-but-real CTAs via MANUALLY_EXPRESSED_CTA (seeded with XAGE5)
  rather than a blanket floor drop. Closes #78.

CTA_gene_names() 258 -> 262. Tests + docs updated; version 1.3.6 -> 1.4.0.

Coverage Stats

2408 of 3400 relevant lines covered (70.82%)

0.71 hits per line

Coverage Regressions

Lines	Coverage	∆	File
23	43.48	-0.71%	partition.py
3	96.51	0.22%	gene_sets.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	26971037794.1	04 Jun 2026 06:21PM UTC	35	70.82	GitHub Action Run

pirl-unc / tsarina / 26971037794
71%

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