目录
dependabot[bot]

build(deps): update itertools requirement from 0.9 to 0.12 (#264)

Updates the requirements on itertools to permit the latest version.

Changelog

Sourced from itertools's changelog.

0.12.1

Added

  • Documented iteration order guarantee for Itertools::[tuple_]combinations (#822)
  • Documented possible panic in iterate (#842)
  • Implemented Clone and Debug for Diff (#845)
  • Implemented Debug for WithPosition (#859)
  • Implemented Eq for MinMaxResult (#838)
  • Implemented From<EitherOrBoth<A, B>> for Option<Either<A, B>> (#843)
  • Implemented PeekingNext for RepeatN (#855)

Changed

  • Made CoalesceBy lazy (#801)
  • Optimized Filter[Map]Ok::next, Itertools::partition, Unique[By]::next[_back] (#818)
  • Optimized Itertools::find_position (#837)
  • Optimized Positions::next[_back] (#816)
  • Optimized ZipLongest::fold (#854)
  • Relaxed Debug bounds for GroupingMapBy (#860)
  • Specialized ExactlyOneError::fold (#826)
  • Specialized Interleave[Shortest]::fold (#849)
  • Specialized MultiPeek::fold (#820)
  • Specialized PadUsing::[r]fold (#825)
  • Specialized PeekNth::fold (#824)
  • Specialized Positions::[r]fold (#813)
  • Specialized PutBackN::fold (#823)
  • Specialized RepeatN::[r]fold (#821)
  • Specialized TakeWhileInclusive::fold (#851)
  • Specialized ZipLongest::rfold (#848)

Notable Internal Changes

  • Added test coverage in CI (#847, #856)
  • Added semver check in CI (#784)
  • Enforced clippy in CI (#740)
  • Enforced rustdoc in CI (#840)
  • Improved specialization tests (#807)
  • More specialization benchmarks (#806)

0.12.0

Breaking

  • Made take_while_inclusive consume iterator by value (#709)
  • Added Clone bound to Unique (#777)

Added

  • Added Itertools::try_len (#723)
  • Added free function sort_unstable (#796)
  • Added GroupMap::fold_with (#778, #785)
  • Added PeekNth::{peek_mut, peek_nth_mut} (#716)
  • Added PeekNth::{next_if, next_if_eq} (#734)
  • Added conversion into (Option<A>,Option<B>) to EitherOrBoth (#713)

... (truncated)

Commits
  • 98d3978 Prepare v0.12.1 release
  • dffac1f Bump obi1kenobi/cargo-semver-checks-action from 2.2 to 2.3
  • 00998a4 CoalesceBy: missing field in Debug
  • a0411d6 CombinationsWithReplacement: use a boxed slice internally
  • 8dd75f1 Permutations: use boxed slices internally
  • b785403 ExactlyOneError: implement Debug differently
  • 7a1c22b FlattenOk: Debug with macro
  • 94452e3 GroupingMapBy: fix Debug implementation
  • 2e325a0 TakeWhileInclusive: missing field in Debug
  • a48c5b4 WithPosition: implement Debug
  • 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 show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
  • @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)

Signed-off-by: dependabot[bot] support@github.com Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

2年前610次提交

Gitpod Ready-to-Code Bioconda downloads Bioconda version install with bioconda Licence GitHub Workflow Status

Rust-Bio-Tools

A set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio. Rust-Bio-Tools provides a command rbt, which currently supports the following operations:

  • a linear time implementation for fuzzy matching of two vcf/bcf files (rbt vcf-match)
  • a vcf/bcf to txt converter, that flexibly allows to select tags and properly handles multiallelic sites (rbt vcf-to-txt)
  • a linear time round-robin FASTQ splitter that splits a given FASTQ files into a given number of chunks (rbt fastq-split)
  • a linear time extraction of depth information from BAMs at given loci (rbt bam-depth)
  • a utility to quickly filter records from a FASTQ file (rbt fastq-filter)
  • a tool to merge BAM or FASTQ reads using marked duplicates respectively unique molecular identifiers (UMIs) (rbt collapse-reads-to-fragments bam|fastq)
  • a tool to generate interactive HTML based reports that offer multiple plots visualizing the provided genomics data in VCF and BAM format (rbt vcf-report)
  • a tool to generate an interactive HTML based report from a csv file including visualizations (rbt csv-report)
  • a tool for splitting VCF/BCF files into N equal chunks, including BND support (rbt vcf-split)
  • a tool to generate visualizations for a specific region of one or multiple BAM files with a given reference contained in a single HTML file (rbt plot-bam)

Further functionality is added as it is needed by the authors. Check out the Contributing section if you want contribute anything yourself. For a list of changes, take a look at the CHANGELOG.

Installation

Requirements

Rust-Bio-Tools depends rgsl which needs GSL to be installed:

  • Ubuntu: sudo apt-get install libgsl-dev
  • Arch: sudo pacman -S gsl
  • OSX: brew install gsl

Bioconda

Rust-Bio-Tools is available via Bioconda. With Bioconda set up, installation is as easy as

conda install rust-bio-tools

Cargo

If the Rust compiler and associated Cargo are installed, Rust-Bio-Tools may be installed via

cargo install rust-bio-tools

Source

Download the source code and within the root directory of source run

cargo install

Usage and Documentation

Rust-Bio-Tools installs a command line utility rbt. Issue

rbt --help

for a summary of all options and tools.

Contributing

Any contributions are highly welcome. If you plan to contribute we suggest installing pre-commit hooks. To do so:

  1. Install pre-commit as explained here
  2. Run pre-commit install in the rust-bio-tools base directory

This should format, check and lint your code when committing.

Authors

关于

用于生物信息学数据处理和分析的Rust工具集

5.7 MB
邀请码
    Gitlink(确实开源)
  • 加入我们
  • 官网邮箱:gitlink@ccf.org.cn
  • QQ群
  • QQ群
  • 公众号
  • 公众号

版权所有:中国计算机学会技术支持:开源发展技术委员会
京ICP备13000930号-9 京公网安备 11010802032778号