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Bump cutadapt from 4.8 to 4.9 #1125

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@dependabot dependabot bot commented on behalf of github Jun 20, 2024

Bumps cutadapt from 4.8 to 4.9.

Changelog

Sourced from cutadapt's changelog.

v4.9 (2024-06-19)

  • Added --action=crop for removing everything except the adapter sequence. (The sequence before and after the adapter is removed.) This can be useful if the "adapter" contains wildcards (such as N) that you are interested in.
  • :issue:788: Added option -L as a counterpart to -l/--length, which allows shortening R1 and R2 to different lengths.
  • A too long minimum overlap is now automatically decreased to the length of the adapter. That is, you can use -a 'ACGT;o=99' to force full-length matches.
  • :issue:784: Fixed some unexpected trimming results for anchored 5' adapters (due to an incorrectly initialized alignment score matrix).
Commits
  • 9276a89 Version 4.9
  • d6e2cbd Decrease too long min. overlap to adapter length
  • 8a54b7a Test on macOS 14 (arm64 runner)
  • 22079ba Add --action=crop
  • b5e74c1 Remove unused test files
  • 40ea156 Add option -L: Allow shortening R1 and R2 to different lengths
  • 7bd8e47 Test --length with paired-end reads
  • 35a4f4a Fix insertion/deletion variable names being mixed up in some places
  • f7bf154 Fix incorrectly initialized score matrix
  • 90a0192 Print both matrices with --debug --debug
  • Additional commits viewable in compare view

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Bumps [cutadapt](https://github.com/marcelm/cutadapt) from 4.8 to 4.9.
- [Release notes](https://github.com/marcelm/cutadapt/releases)
- [Changelog](https://github.com/marcelm/cutadapt/blob/main/CHANGES.rst)
- [Commits](marcelm/cutadapt@v4.8...v4.9)

---
updated-dependencies:
- dependency-name: cutadapt
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jun 20, 2024
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