27345096047
77%

Ran 11 Jun 2026 11:58AM UTC

Jobs 1

Files 38

Run time 1min

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Committed 11 Jun 2026 11:57AM UTC coverage: 73.757% (-0.4%) from 74.147%

Build # 27345096047

Build Type

push

github

Committed by

web-flow

Commit Message

Add fragment-model QC; refuse stub gene models at addition time (closes #108) (#113)

GAGE12B (tsarina#108) was a degenerate 117-bp gene model (7-aa ORF) that
slipped in on HPA gene-level nTPM. Add tsarina/qc.py with an injectable
fragment detector and wire a hard guard into add_cta_gene.build_row that
refuses any candidate whose longest pyensembl protein is below a floor.

- Absolute floor (30 aa), not the #108 family-median heuristic: real CTAs
  can be genuinely small (PRM1=51 aa is the smallest in the table; several
  SPANX/XAGE at 72-81), so a family-relative rule risks flagging them. The
  floor sits well above the fragment (7 aa) and below the smallest real CTA.
- length_fn is injectable so the flagging logic is unit-tested in CI, which
  does not download pyensembl data; one integration test hits real pyensembl
  and skips when absent (incl. a table-wide no-fragments check).

Version: 1.13.0 -> 1.14.0.

Coverage Stats

2715 of 3681 relevant lines covered (73.76%)

0.74 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	27345096047.1	11 Jun 2026 11:58AM UTC	38	73.76	GitHub Action Run

pirl-unc / tsarina / 27345096047
77%

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