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osteosarc 0.1.3

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@iskandr iskandr released this 21 Sep 19:54
v0.1.3
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Fixes mitochondrial annotation in Variants.to_varcode(): chrM and M now convert to Ensembl's MT through Varcode's existing converter. The original contig name and all source entries remain available in provenance.

Custom references can disable convert_ucsc_contig_names and normalize_contig_names to preserve literal names. Scaffold names are no longer altered by unconditional chr stripping. The docs explain these options and the limits of alias conversion.

Includes mitochondrial annotation regressions and consumer CI with Varcode 7.0.0 and 9.3.7. The reported chrM:12994 G>A variant was verified against Ensembl 95 as MT-ND5 p.A220T.

Install or update with python -m pip install --upgrade osteosarc.

Fixes #8 through PR #9.

Known live-data issue: fresh snapshots currently flag eight stale correction rules after upstream source changes. This also affected 0.1.2 and is tracked separately in #10. Existing pinned snapshots remain usable.

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