wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
309 stars 31 forks source link

build(deps): update rust-htslib requirement from 0.26.* to 0.30.* #28

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

Updates the requirements on rust-htslib to permit the latest version.

Changelog

Sourced from rust-htslib's changelog.

[0.30.0] - 2020-04-03

Changes

  • Removed fn header_mut() from bam::Read trait.
  • Fixed a major performance regression when reading bam files (issue #195).

[0.29.0] - 2020-03-26

Changes

  • Migrate buffer intervals to u64.

[0.28.0] - 2020-03-26

Changes

  • Return u64 wherever htslib has migrated to using 64 bit.
  • Implement more bio-types (Interval, Locus, Strand).

[0.27.0] - 2020-03-17

Changes

  • Updated to Htslib 1.10.2.
  • bam::Record.set() will panic if seq.len() != qual.len(). Previously, mismatched length would cause uninitialized memory to be written into the BAM file.
  • use serde_bytes to serialize .data section of bam::Record when using serde - large speed improvement.
  • change build.rs to avoid re-running when htslib or wrapper.h haven't changed.
  • update some dependencies.
  • refactor native dependency into htslib-sys crate, for greater versioning flexibility
  • Record::from_sam require &mut HeaderView. Provide the appropriate accessor.
  • set() no longer invalidates tag data.
  • Various minor improvements.

[0.26.1] - 2019-12-03

Changes

  • Various bug fixes in CIGAR string handling, INFO tag reading and FORMAT tag reading.

[0.26.0] - 2019-09-27

Changes

  • Allow caching of CIGAR in bam::RecordBuffer.

[0.25.0] - 2019-09-27

Changes

  • Migrated error handling to the snafu crate: https://docs.rs/snafu.
  • Cleaned up and simplified API (including breaking changes).
  • Allow writing SAM files from the bam::Writer.

[0.24.0] - 2019-05-31

Added

  • Allow setting unmapped BAM record (without Cigar string).
  • Various bug fixes and error handling improvements.
  • Various Pysam-derived methods for interpreting Cigar strings.

[0.23.0] - 2019-05-02

Added

  • Support for BAM indices that are not placed beside a file.bam as file.bam.bai
... (truncated)
Commits
  • df0c493 release version 0.30.0
  • 58a5ef8 update changelog
  • 3fa020d fix issue #195.
  • b12b363 (cargo-release) start next development iteration 0.29.1-alpha.0
  • 661292c release version 0.29.0
  • e81ae83 return target_len as u64
  • ff69080 update changelog
  • 1c2c676 migrate remaining positions to u64
  • fb669a7 (cargo-release) start next development iteration 0.28.1-alpha.0
  • c424ce3 release version 0.28.0
  • Additional commits viewable in compare view


Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.


Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language - `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com): - Update frequency (including time of day and day of week) - Pull request limits (per update run and/or open at any time) - Out-of-range updates (receive only lockfile updates, if desired) - Security updates (receive only security updates, if desired)
wwood commented 4 years ago

See #24

dependabot-preview[bot] commented 4 years ago

OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting @dependabot ignore this major version or @dependabot ignore this minor version.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.