1
94%
master: 94%

Ran 14 May 2026 04:11PM UTC

Files 60

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Committed 14 May 2026 04:07PM UTC coverage: 93.592% (+0.08%) from 93.517%

Job # 25870885559.1

Build Type

Pull #183

github

Committed by

iskandr

Commit Message

test_read_phasing: add synthetic somatic+germline phasing test

Builds a synthetic mini-BAM (via MockAlignmentFile + make_pysam_read)
with reads spanning an imagined somatic SNV at chr1:4 (T>G) and a
nearby germline SNP at chr1:8 (T>A): three reads carry both alts,
two carry the somatic alt only, two carry the germline alt only.

Walks the full ReadCollector -> annotate_phased_variants ->
IsovarReadPhasing stack and verifies the somatic and germline calls
are reported as in-cis partners.

This is the canonical motivating scenario for openvax/varcode#268's
germline-aware effect prediction: a somatic mutation whose codon
overlaps a germline polymorphism, where the protein outcome depends
on whether the two are in cis -- and only RNA-read co-occurrence
disambiguates.

Pull Request Pull Request #183: Add IsovarReadPhasing adapter for RNA-read variant phasing

Coverage Stats

2556 of 2731 relevant lines covered (93.59%)

0.94 hits per line

openvax / isovar / 25870885559 / 1
94%
master: 94%

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Source Files on job 25870885559.1

openvax / isovar / 25870885559 / 1 94% master: 94%

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Markdown

Textile

RDoc

HTML

Rst

Source Files on job 25870885559.1

openvax / isovar / 25870885559 / 1
94%
master: 94%

README BADGES
x