v0.13.0: Add --split-window for split-by-low-quality trimming

The split-by-low-quality approach previously split a read on any single
base below --cutoff, with no notion of a minimum run of low-quality bases.

Add --split-window (default 1, preserving the old behavior): a read is
only split once a run of consecutive sub-cutoff bases reaches the window
length. Shorter dips are tolerated and kept inside the segment; leading
and trailing low-quality bases are still trimmed.

Also warn on stderr when a trimming argument (--cutoff, --headcrop,
--tailcrop, --split-window) is set but ignored by the selected approach,
or because no --trim-approach was given.

Bump version to 0.13.0 and apply cargo fmt across the crate.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

v0.12.0b

Full Changelog: v0.12.0...v0.12.0b

Changes from @MillarCD making chopper faster again!

v0.12.0: Merge pull request #54 from MillarCD/master

Improve runtime performance by adding channels

v0.11.0

implementation of finding good segments split by low quality interrup…

v0.10.0b

Add a --trim option to use quality score for trimming from read ends (#51)

Full Changelog: v0.9.2...v0.10.0b

v0.9.2

Remove the explicit max i32 as a default value for max length, and some other optimizations

Full Changelog: v0.9.1...v0.9.2

v0.9.1

Full Changelog: v0.9.0...v0.9.1

Update

What's Changed

• Add GC content parameter --mingc --maxgc by @JMencius in #30
• enhance -i performace by @JMencius in #32
• add gzip/xz/bzip2 support for input by @sharkLoc in #34

New Contributors

• @sharkLoc made their first contribution in #34

Full Changelog: v0.8.0...v0.9.0

Let me know if a musl build is necessary for someone!

update

This release includes multithreaded minimap2 for contamination checking as contributed by @Ge0rges and reading from a file (rather than stdin) as contributed by @JMencius

What's Changed

• Make use of faster preset and multithreaded minimap2 by @Ge0rges in #26
• Add straightforward --input by @JMencius in #29

New Contributors

• @Ge0rges made their first contribution in #26
• @JMencius made their first contribution in #29

Full Changelog: v0.7.0...v0.8.0

cigar-level alignment for removing contaminants

In some cases contaminants were not removed #19, and to solve this alignment accuracy is improved by using with_cigar()