Test RNA phasing on complete real Sid templates - #573
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Varcode's shared Sid tests covered mutation targets and junction records, but RNA phasing still relied on synthetic alignments. Add integration tests using three verified
openvax-v2members: paired short-read NTF3, ONT NTF3, and ONT EXOC4.The tests pin independently audited fragment counts and exercise cis, trans, unknown phase, minimum-fragment thresholds, both query orders, and
MolecularPhaseResolver. They compare exact record multiplicities with the manifest and with every record of each selected RG/QNAME in the bundle source, checking mate retention and supplementary-record filtering. The test guide records sources, alleles, expectations, evidence settings, and reproduction. Companion alleles are RNA observations, without an assumed germline/somatic classification.Validation:
./lint.shpassed; the new integration coverage and existing phasing tests passed (70 tests);TEST_SH_MAX=2 ./test.shpassed (3,205 tests). GitHub's existing Python 3.9–3.11 matrix also runs these tests from the source distribution.Patch release: 10.11.5.
Closes #528.