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refactor(compare,fastq) + test: in-process Command::execute for Phase 3 (#352) - #355

Merged

nh13 merged 17 commits into

mainfrom

nh/issue-352-phase-3

May 22, 2026

Merged

refactor(compare,fastq) + test: in-process Command::execute for Phase 3 (#352)#355
nh13 merged 17 commits into
mainfrom
nh/issue-352-phase-3

Commits on May 21, 2026
- test(clip): invoke clip Command::execute in-process
  nh13
  committed
  65985d4
- test(dedup): invoke dedup Command::execute in-process
  nh13
  committed
  0cf1ecf
- test(correct): invoke correct Command::execute in-process
  nh13
  committed
  eaea8de
- test(group): invoke group Command::execute in-process
  nh13
  committed
  88d0b9d
- test(filter): invoke filter Command::execute in-process
  nh13
  committed
  d3c90a8
- test(extract): invoke extract Command::execute in-process
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  committed
  04adadd
- test(simplex): invoke simplex Command::execute in-process
  nh13
  committed
  532b063
- test(simplex-metrics): invoke simplex-metrics Command::execute in-process
  nh13
  committed
  6f8e9f5
- test(duplex): invoke duplex Command::execute in-process
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  committed
  e709527
- test(duplex-metrics): invoke duplex-metrics Command::execute in-process
  nh13
  committed
  17675ee
- test(codec): invoke codec Command::execute in-process
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  committed
  e6d29c2
- test(review): invoke review Command::execute in-process
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  committed
  bb40c3b
- refactor(compare)!: return CompareMismatch instead of process::exit
  nh13
  committed
  89258a7
- test(compare): invoke compare bams Command::execute in-process
  nh13
  committed
  832c42a
- feat(fastq): add --output/-o flag for file output
  nh13
  committed
  ba63851
- test(fastq): invoke fastq Command::execute in-process
  nh13
  committed
  8e7aba1
- test(zipper): invoke zipper Command::execute in-process for non-stdin tests
  nh13
  committed
  b964c20

Commits

Commits on May 21, 2026