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Reject contradictory RNA fragment alleles in phasing and support (10.10.2) - #564
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A fragment with an alternate-supporting mate and a contradictory reference/third-allele mate was counted as clean alternate support. This could return definite cis with no unambiguous molecules. Require agreement among quality-passing observations within each read-group/QNAME fragment for both support counts and phase calls.
Registered haplotypes still require a complete context on one alignment. A fully covered, high-quality contradictory mate now vetoes the fragment; missing/low-quality context does not. Distinguish informative other alleles from unavailable evidence without treating anchored nonmatches as reference/trans. Independent clean fragments still rescue support.
Closes #557. Bumps Varcode to 10.10.2; depends on #562 and must merge/release after 10.10.1.
Validation: 14 new regression cases failed on the previous implementation; targeted phasing/haplotype suite now 86 passed.
./lint.shand full./test.sh -q -n 2pass (3,086 tests on current main plus #562, pandas 3.0.6). CI verifies the supported Python matrix and cross-annotator parity before publication.