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Follow-up review fixes for noodles BAM migration (#115) - #117

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ewels wants to merge 5 commits into

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review/pr115-followup

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Follow-up review fixes for noodles BAM migration (#115)#117
ewels wants to merge 5 commits into
mainfrom
review/pr115-followup

Commits on Jun 16, 2026
- Migrate BAM I/O from rust-htslib to noodles (#115)
  
  ewels
  and
  cursoragent
  authored
  9cf5121
- ci: harden GitHub Actions workflows (zizmor) (#116)
  
  ewels
  and
  claude
  authored
  2556c9d
- fix(bam): harden noodles compatibility shim from PR #115 review
  
  ewels
  and
  claude
  committed
  ea20e9b
- perf(bam): stream indexed reads instead of buffering whole references
  
  ewels
  and
  claude
  committed
  ddfe71a
Commits on Jun 17, 2026
- perf(bam): stream CRAM reads via self-referential cursors
  
  ewels
  and
  claude
  committed
  da62350