openvax / isovar / 25870306393

94%

master: 94%

Pull #183

github

test_read_phasing: cover real upstream phasing logic

The b16 fixture has four variants on four different chromosomes, so
`run_isovar` against it never produces non-empty
`phased_variants_in_supporting_reads` -- the b16 tests verify wiring
but not phased-partner behavior end-to-end.

Add two integration tests that drive
`isovar.phasing.annotate_phased_variants` directly with hand-rolled
results sharing alt-read names, then exercise `IsovarReadPhasing`
against the annotated output:

  * test_adapter_consistent_with_annotate_phased_variants verifies
    the adapter exposes exactly what the upstream pipeline populates,
    on a v1<-(r12a,r12b)->v2<-(r23)->v3 topology that v1/v3 don't
    directly bridge.
  * test_adapter_respects_min_shared_fragments_threshold verifies a
    single shared read below threshold yields no partners.

Also relabel the b16 block as a pipeline smoke test and point readers
at the new integration tests for phased-partner coverage.

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

2556 of 2731 relevant lines covered (93.59%)

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