Bump cutadapt from 3.7 to 4.5

[dependabot[bot]]

Bumps cutadapt from 3.7 to 4.5.

Release notes

Sourced from cutadapt's releases.

Version 4.0

GitHub releases are made irregularly and exist only to be able to provide a single-file Windows executable for Cutadapt, which is not as well tested as the other installation methods.

Changelog

Sourced from cutadapt's changelog.

v4.5 (2023-10-06)

• :pr:725: Added a --max-average-error-rate/--max-aer option to add a filter that checks if the number of expected errors divided by read length is above a certain threshold. The expected errors are calculated the same as in --max-expected-errors, and dividing by read length helps for reads that have varying lengths.
• :issue:696: Added a histogram of the lengths of removed poly-A tails to the report.
• :issue:696: For paired-end data, --poly-a was changed to trim poly-T "heads" on R2 (this is still experimental as it is unclear whether that is the desired behavior. Please give feedback!)
• A poly-A tail is only removed if it is at least three nucleotides long.
• :issue:734: Fixed misassignments during demultiplexing that would sometimes happen when there are collisions between adapter sequences (when the warning "sequence ... cannot be assigned uniquely" was printed). Previously, sequences could incorrectly be assigned to an adapter that is not actually the best match.

v4.4 (2023-04-28)

• :issue:695: Fixed very slow k-mer heuristic initialization (hours instead of seconds) for degenerate adapter sequences such as A{100} as used when doing poly-A trimming.
• :issue:696: Added option --poly-a for trimming poly-A tails. This is more accurate and multiple times faster than using -a A{100} as previously recommended. This is currently experimental (that is, the algorithm may change in the next one or two releases).
• :issue:685: Sped up index generation somewhat. This is most noticable when demultiplexing using thousands or more adapters. The speedup is different depending on whether indels are allowed or not because different algorithms are used.
• :issue:685: Sped up demultiplexing (when using an index) for the case when the read contains N bases within the region where the adapter matches. Previously, any N would disable the index for that read and trigger a fallback to the slow method of matching each adapter one-by-one. Now the index is used even in those cases.
• :pr:700: Sped up --max-expected-errors. Thanks @​rhpvorderman.

v4.3 (2023-03-17)

• :pr:663: Cutadapt became significantly faster due to an added runtime heuristic that avoids running the full alignment algorithm if it can be proven that it cannot succeed. Thanks to @​rhpvorderman for this great improvement!
• :issue:665: 5' adapters did not allow partial matches in the beginning when the :ref:rightmost <rightmost> adapter-search parameter was used.

... (truncated)

Commits

• e04cc32 Bump cibuildwheel
• 22f20e4 Changelog
• 0b9c325 Add repo to project URLs
• 511a8d2 Fix colliding sequences in the index not being added to the index at all
• ed7ec8d Merge pull request #733 from marcelm/doc
• 722c2af Add sphinx-rtd-theme
• bd12117 Make Renamer picklable
• 2b85d65 Test --rename with multiple cores
• 2cd48dd Merge pull request #727 from rhpvorderman/usedoubles
• ddbe8fd Merge pull request #731 from marcelm/rhpvorderman-patch-1
• Additional commits viewable in compare view

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[codecov[bot]]

Codecov Report

All modified lines are covered by tests :white_check_mark:

Comparison is base (2c4a709) 86.43% compared to head (ef96056) 86.43%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1022 +/- ## ======================================= Coverage 86.43% 86.43% ======================================= Files 28 28 Lines 6110 6110 ======================================= Hits 5281 5281 Misses 829 829 ```

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[Donaim]

@dependabot rebase

[dependabot[bot]]

Superseded by #1048.