openvax / isovar / 25948671991

Builds Branch Commit Type Ran Committer Via Coverage
25948671991 master Add docs regression checks Add tests covering corrected documentation for run_isovar, README filter flags, and DataFrameBuilder.exclude; bump isovar to 1.7.1. push web-flow github
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25948539954 codex/docs-cleanup-129-133-135 Add docs regression checks Pull #187 iskandr github
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25942770579 master Add Isovar mutant transcript source Replace VarcodeAdapter with a focused IsovarMutantTranscript source, keep read phasing on IsovarReadPhasing, make the split providers compose safely, and require varcode>=5.0.0. push web-flow github
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25942541389 codex/mutant-transcript-source Fix provider composition for read evidence Pull #186 iskandr github
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25925535425 codex/mutant-transcript-source Add Isovar mutant transcript source Pull #186 iskandr github
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25885451011 master Merge pull request #185 from openvax/bump-1.6.0 Bump version to 1.6.0 for IsovarReadPhasing (#183) push web-flow github
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25884370763 bump-1.6.0 Bump version to 1.6.0 for IsovarReadPhasing (#183) Pull #185 iskandr github
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25882603005 master Merge pull request #183 from openvax/read-phasing-adapter Add IsovarReadPhasing adapter for RNA-read variant phasing push web-flow github
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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
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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
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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
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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
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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
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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
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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
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