osteosarc 0.1.1

Use datacache for downloads and browse samples before fetching reads around selected variants.

python -m pip install osteosarc==0.1.1

• Datacache handles full-file downloads and validation. Existing 0.1.0 snapshots, shared cache objects, and read subsets remain usable.
• Pysam is a standard dependency; [reads] remains a compatibility alias.
• data.describe_samples() lists samples and sequencing types. data.assets_for_sample(...) selects their files, and data.extract_reads(source, variants=targets, padding=100) fetches regional reads.
• Required SAMtools capabilities are checked before acquisition, including paired mates and barcode filters. Fixes #3.
• Malformed VAF rows or positions leave an explicit non-ready entry and diagnostics while valid entries remain available. Pass TSV text to parse_variants(index, vaf_tsv) or use Dataset.variants(). Generic parse_table stays strict by default. Fixes #4.
• Cached receipt sizes are checked even when a file's digest has already been verified.
• Shorter README and documentation organized around runnable examples. osteosarc samples now prints a readable table; use samples --json for the previous source claims.

Validation: 105 local tests, 71 runnable documentation examples, Python 3.10/3.12/3.13 CI, and consumer integration checks. Topiary 5.66.0 passed the seven consumer tests after explicitly replacing its pinned Osteosarc for runtime testing; its dependency pin must be updated for a normal 0.1.1 installation.

The five unresolved alleles in #5 retain their existing statuses and provenance. Full vaccine ranking is downstream work.

Documentation · PyPI · Changes