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subset_bundleandtest-data make --fromcarve out members offline while
preserving original source headers, acquisition receipts and selection results (#90).- New
sv-regressions-v2panel 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openvax-v3 read specification is an unpublished candidate.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The comprehensive openvax-v3 read bundle remains unpublished and is being completed separately.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.