Osteosarc 0.2.5

Adds the SV interest catalogue and lets the command line run the whole quickstart.

python -m pip install --upgrade osteosarc==0.2.5

• SV interest catalogue (#29): 637 structural-variant nominations from the September 22, 2026 audit. Each has its original calls, breakend geometry, Ensembl 115 annotation, T2 gene expression and RNA evidence scoped to its source. It loads offline with load_sv_interest() or load_panel("sv-interest-v1").
• CLI parity with the Python quickstart (#33, fixes #30):
  • osteosarc assets SNAP --sample T0_tumor … lists a sample's registry-linked files.
  • osteosarc reads SNAP BAM --variant ID [--variant ID …] --padding N fetches reads around catalogue variants. It shares one cache entry with Dataset.extract_reads(variants=..., padding=...).
  • Adds osteosarc --version, and help text for timepoints and vaccines.
  • Explicit regions still need --assembly, and can now appear before or after options on every supported Python.

Validation:

• CI passes on Python 3.9–3.13, including Varcode 7/9 consumer checks.
• 245 tests pass against the built wheel in a clean virtualenv outside the checkout. The 17 skips need optional consumer packages, which CI covers.
• The installed CLI was tested against live data: assets --sample, two-variant reads --variant, and explicit regions after --assembly.

Documentation · PyPI

https://claude.ai/code/session_01CcNHdiWgNhPGLmd4kDvG9G