1
77%
main: 77%

Ran 11 Jun 2026 07:32PM UTC

Files 38

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Committed 11 Jun 2026 07:31PM UTC coverage: 73.971% (+0.09%) from 73.88%

Job # 27372254080.1

Build Type

push

github

Committed by

web-flow

Commit Message

Add opt-in relaxed reproductive tier + document ERV verdicts (closes #119) (#122)

Addresses the ERV env-gene review:

- Ask 3 (less-stringent tier): CTA_relaxed_reproductive_gene_names/_ids(
  min_deflated_frac=0.80) -- RNA-only candidates that fail the default
  reproductive gate but keep a dominant testis/placenta signal. Restricted to
  RNA-only genes so the failure is the RNA fraction, not somatic protein
  detection. Includes syncytin-1/2 (ERVW-1/ERVFRD-1); ERVV-1 at 0.90. Opt-in,
  disjoint from default sets.
- Ask 1 (ERVV-1): correctly fails -- not 'more restricted' than ERVH48-1; its
  placental signal (15.5) is far weaker (148), so the same leak is a larger
  fraction. Documented, not hand-included.
- Ask 2 (restriction vs passes_filters): documented as by-design -- categorical
  somatic label vs deflated-fraction gate measure different things.
- Ask 4 (RNA-only confidence): documented; deliberately NOT blanket-capped (24
  strong clean RNA-only CTAs like TEX38@377nTPM would be wrongly downgraded;
  only sub-floor RNA is capped, per #114). The RNA-only status is queryable.

Version: 1.16.0 -> 1.17.0.

Coverage Stats

2751 of 3719 relevant lines covered (73.97%)

0.74 hits per line

pirl-unc / tsarina / 27372254080 / 1
77%
main: 77%

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Markdown

Textile

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Source Files on job 27372254080.1

pirl-unc / tsarina / 27372254080 / 1
77%
main: 77%

README BADGES
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