All pull requests

Pull requests

• Fix one-gap adapter search offset (#728) and speed up matchWithOneInsertion

  #729·dougnukem opened Sep 29, 2026Contributor·

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• ci: thread-count correctness checks (would catch #721) and base-vs-head benchmarks

  #727·dougnukem opened Sep 28, 2026Contributor·

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• fix: bound in-flight memory at high thread counts (stacked on #723)

  #726·dougnukem opened Sep 28, 2026Contributor·

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• test: benchmark corpus + historical release backfill (independent of #723)

  #725·dougnukem opened Sep 28, 2026Contributor·

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• Return a nonzero exit status for detected paired-end read-count mismatches

  #719·thierrygosselin opened Sep 6, 2026·

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• Return a nonzero exit status for detected FASTQ parsing errors

  #718·thierrygosselin opened Sep 6, 2026·

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• Reject truncated BGZF blocks instead of treating them as EOF

  #717·thierrygosselin opened Sep 6, 2026·

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• Fix undetected buffered output-write failures

  #716·thierrygosselin opened Sep 6, 2026·

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• Count reads dropped by --dedup as duplicates instead of "passed filter" (#638, #528)

  #715·cindykrafft opened Sep 4, 2026·

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• Add --umi_tag option to output UMI as a SAM-style tag (e.g. XR:Z:UMI)

  #713·yangmqglobe opened Aug 22, 2026·

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• Enable zstd compression format

  #640·GilbertHan1011 opened Nov 19, 2025·

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• Makefile: Respect build environment, add destdir support

  #619·outpaddling opened Jun 21, 2025·

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• Use EX_USAGE for missing arguments in main()

  #615·hayzamjs opened Jun 17, 2025·

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• feat: sets trim-poly-G as True for one-color-system too (iSeq 100)

  #598·Coppini opened Feb 20, 2025·

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• Added a new function(umi_skipb) to the program to skip the specified bp number before trim the UMI sequence.

  #550·biolxy opened Mar 8, 2024·

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• cuting doesn't interfere with deduplication

  #545·SilasK opened Feb 9, 2024·

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• check read errors in fastqreader

  #533·jchorl opened Nov 15, 2023·

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• Add a Docker container

  #527·maol-corteva opened Oct 11, 2023·

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• fix average q-score calculation

  #495·DrinnanSante opened May 31, 2023·

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• Add args for adjusting mismatch number

  #311·y9c opened Jan 4, 2021Contributor·

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