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osteosarc 0.15.0

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@iskandr iskandr released this 30 Sep 02:02
60a25a4
  • subset_bundle and test-data make --from carve out members offline while
    preserving original source headers, acquisition receipts and selection results (#90).
  • New sv-regressions-v2 panel supplies the three Isovar fusions' retained sides;
    newly requested fusion bundles use it. Published v1 panels and bundles stay unchanged (#96).
  • Historical retrieval cases have verified native coordinates, exact BAM contig names,
    mitochondrial reference identity and a guard against incompatible merges (#99).
  • Reviewed Tempus evidence overlap is available on files and file selections, with
    explicit preference required to exclude one product. Both original labels and
    acquisition receipts remain intact; the true sample identity is still unresolved (#100).
  • Python 3.14 support: the tests run on Python 3.9 to 3.14.
  • Comprehensive vaccine/RNA test corpus: 51 vaccine-associated variants from the
    union of membership sources, a complete per-BAM support matrix, four
    DNA-supported SNVs with zero reported RNA alternate reads, a historical RNA
    disagreement case, frameshifts and SV evidence. Its
    openvax-v3 read specification is an unpublished candidate.
  • Shared read builds can checkpoint completed source selections and set their
    supplementary-alignment depth and region limits explicitly in the spec.
  • Compact carry-forward preserves query positions for placed-unmapped records.
    Comprehensive control audits verify source URLs and BAM/index checksums against
    acquisition receipts; packaged RNA-support claims follow the actual recounts.

Validation: 377 tests pass, including receipt attribution, native-coordinate retrieval, source overlap, and placed-unmapped regression checks. The complete evidence delivery reproduces 140 control recounts, including 60 RNA-negative checks.

The comprehensive openvax-v3 read bundle remains unpublished and is being completed separately. Issue #100 remains open for specimen/timepoint documentation.