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@dependabot dependabot bot commented on behalf of github Sep 22, 2025

Bumps bio from 1.6.0 to 3.0.0.

Changelog

Sourced from bio's changelog.

3.0.0 (2025-09-19)

⚠ BREAKING CHANGES

  • improved API and internals for pattern_matching::myers and add LazyMatches::dist_at() (#640)

Features

  • Added BEDPE file support (#631) (61adf2a)
  • improved API and internals for pattern_matching::myers and add LazyMatches::dist_at() (#640) (122a44d)

2.3.0 (2025-05-09)

Features

  • Add BLOSUM30 and BLOSUM45 substitution matrices (#630) (6188ea7)
  • POA, without saving traceback (#620) (ac8fd53)

Dependencies

  • update petgraph requirement from >=0.4, <0.8 to >=0.4, <0.9 (#632) (a22f946)

2.2.0 (2025-02-26)

Features

  • FASTA/FASTQ unification (#433) (734d6d1)
  • position-specific scoring matrix: support inputs with ambiguous monomers in from_seqs (#616) (050b154)
  • Reverse qgrams iterator (#521) (46382ba)
  • Write fasta with fix line width (#490) (2e66911)

Dependencies

  • update ordered-float requirement from 4.2 to 5.0 (#623) (8e188f5)
  • update thiserror requirement from 1 to 2 (#608) (68fd94f)

2.1.0 (2025-02-24)

Features

  • Implementing From and TryInto for Phase (#618) (12dd1bd)

Dependencies

... (truncated)

Commits
  • 14c0425 chore(master): release 3.0.0 (#646)
  • 61adf2a feat: Added BEDPE file support (#631)
  • 122a44d feat!: improved API and internals for pattern_matching::myers and add LazyMat...
  • 0a36bcf refactor: Clippy warnings caused by legacy numeric constants (#644)
  • a56a02a refactor: removed lazy_static! dependency and cleaned up scores (#639)
  • 225f3f5 chore(master): release 2.3.0 (#633)
  • ac8fd53 feat: POA, without saving traceback (#620)
  • a22f946 deps: update petgraph requirement from >=0.4, <0.8 to >=0.4, <0.9 (#632)
  • 2cb4536 build(deps): Remove unused dependency rand (#635)
  • 64c5327 update lazy-static (#634)
  • Additional commits viewable in compare view

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Bumps [bio](https://github.com/rust-bio/rust-bio) from 1.6.0 to 3.0.0.
- [Release notes](https://github.com/rust-bio/rust-bio/releases)
- [Changelog](https://github.com/rust-bio/rust-bio/blob/master/CHANGELOG.md)
- [Commits](rust-bio/rust-bio@v1.6.0...v3.0.0)

---
updated-dependencies:
- dependency-name: bio
  dependency-version: 3.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
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dependabot bot commented on behalf of github Sep 22, 2025

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@dependabot dependabot bot mentioned this pull request Sep 22, 2025
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