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fix(bam): prevent duplicate reads from indexed CRAM queries - #178

Draft

NicoDeVeaux wants to merge 5 commits into

ndv/fix-pr118-unmapped-sweepfrom

ndv/fix-pr118-cram-multiref-fetch

Draft

fix(bam): prevent duplicate reads from indexed CRAM queries#178
NicoDeVeaux wants to merge 5 commits into
ndv/fix-pr118-unmapped-sweepfrom
ndv/fix-pr118-cram-multiref-fetch

Commits on Oct 23, 2026
- test(bam): per-reference CRAM fetch must return only that reference's records
  
  NicoDeVeaux
  and
  claude
  committed
  91b4479
- fix(bam): per-reference CRAM fetch keeps only that reference's records
  
  NicoDeVeaux
  and
  claude
  committed
  82fdd56
Commits on Nov 1, 2026
- fix(bam): read each CRAM reference container once
  NicoDeVeaux
  committed
  41c84c7
- chore(bam): merge updated unmapped sweep base
  NicoDeVeaux
  committed
  234b5f8
- chore(bam): merge current CI fixes from unmapped sweep base
  NicoDeVeaux
  committed
  be39763