openvax / isovar
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LAST BUILD ON BRANCH read-phasing-adapter
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coverage: 93.592% (+0.08%) from 93.517%
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Source Files on read-phasing-adapter

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Builds Branch Commit Type Ran Committer Via Coverage
25880618441 read-phasing-adapter read_phasing: soften forward-looking docstring claim Phrase the relationship as "implements the shape that varcode adopts in #378/#379" rather than "satisfies varcode's ReadPhasingSource Protocol", so a reader who lands on master between isovar#1... Pull #183 iskandr github
93.59
25878070721 read-phasing-adapter read_phasing: align docstring with varcode's generic phasing API Varcode is dropping Isovar-named identifiers from its public surface (openvax/varcode#378, openvax/varcode#379). Replace the docstring reference to the old `IsovarAssemblyProvider` ... Pull #183 iskandr github
93.59
25875420802 read-phasing-adapter read_phasing: rename threshold test; document has_evidence/partners interface * Rename test_adapter_respects_min_shared_fragments_threshold to test_threshold_filter_propagates_through_adapter and explain that the adapter is passive here -- th... Pull #183 iskandr github
93.59
25870885559 read-phasing-adapter 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 read... Pull #183 iskandr github
93.59
25870306393 read-phasing-adapter 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... Pull #183 iskandr github
93.59
25869620150 read-phasing-adapter read_phasing: add b16 end-to-end tests; drop docstring overspecification - Add four integration tests that exercise IsovarReadPhasing through a full run_isovar invocation on the b16 RNA fixture (same data the varcode_adapter tests use). Cover... Pull #183 iskandr github
93.59
25865528272 read-phasing-adapter read_phasing: runnable doctest, document duck-typed contract, add __repr__ - Replace the broken docstring example (referenced undefined names) with a doctest-runnable one built on SimpleNamespace, executed via a dedicated `test_docstring_exam... Pull #183 iskandr github
93.59
25857611734 read-phasing-adapter Add IsovarReadPhasing adapter for RNA-read variant phasing Exposes IsovarResult.phased_variants_in_supporting_reads through a narrow has_evidence/partners_in_cis interface, suitable as a read- phasing source for varcode's germline-aware effect pr... Pull #183 iskandr github
93.59
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