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fix(flagstat): match samtools counts, alignment priority and percentages - #175

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NicoDeVeaux wants to merge 5 commits into

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ndv/fix-flagstat-qcfail-proper-dup

Draft

fix(flagstat): match samtools counts, alignment priority and percentages#175
NicoDeVeaux wants to merge 5 commits into
mainfrom
ndv/fix-flagstat-qcfail-proper-dup

Commits on Oct 23, 2026
- test(flagstat): pin samtools parity for QC-failed, proper-pair and duplicate counts
  
  NicoDeVeaux
  and
  claude
  committed
  b8c527b
- fix(flagstat): split counts by QC pass/fail and follow samtools' flagstat_loop
  
  NicoDeVeaux
  and
  claude
  committed
  2bd1209
Commits on Oct 30, 2026
- fix(deps): update vulnerable crossbeam-epoch and libz-sys
  NicoDeVeaux
  committed
  b5658a8
Commits on Oct 31, 2026
- fix(flagstat): combine QC counts with samtools alignment priority
  NicoDeVeaux
  committed
  c1adcf9
- chore(lint): iterate corresponding count arrays
  NicoDeVeaux
  committed
  a9083c5