openvax / isovar / 25870885559

94%

master: 94%

Pull #183

github

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.

16 of 16 new or added lines in 2 files covered. (100.0%)

2556 of 2731 relevant lines covered (93.59%)

0.94 hits per line