wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
297 stars 30 forks source link

build(deps): update rust-htslib requirement from 0.26.* to 0.29.* #23

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.

[0.29.0] - 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
  • Implement SequenceRead trait for BAM records.
  • Add function to build an index for a BAM file.
  • CRAM support for BAM reader and writer.

Changes

  • Allow to specify particular index filename when instantiating a BAM reader.
... (truncated)
Commits
  • 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
  • 8d19abd fix tests
  • 7530cc8 update changelog
  • 6c537a0 implement various bio-types (interval, locus, strand)
  • 3100b8c revert to using ret.
  • 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.


Note: This repo was added to Dependabot recently, so you'll receive a maximum of 5 PRs for your first few update runs. Once an update run creates fewer than 5 PRs we'll remove that limit.

You can always request more updates by clicking Bump now in your Dependabot dashboard.

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)
dependabot-preview[bot] commented 4 years ago

Superseded by #28.