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Open Source Science

https://github.com/brentp/goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

https://github.com/brentp/goleft

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.8%) to scientific vocabulary

Keywords

bioinformatics coverage depth genomics golang
Last synced: 5 months ago · JSON representation

Repository

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Basic Info
  • Host: GitHub
  • Owner: brentp
  • License: mit
  • Language: Go
  • Default Branch: master
  • Homepage:
  • Size: 5.11 MB
Statistics
  • Stars: 220
  • Watchers: 16
  • Forks: 25
  • Open Issues: 16
  • Releases: 26
Topics
bioinformatics coverage depth genomics golang
Created over 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

goleft

Build Status

goleft is a collection of bioinformatics tools written in go distributed together as a single binary under a liberal (MIT) license.

Running the binary goleft will give a list of subcommands with a short description. Running any subcommand without arguments will give a full help for that command.

Installation

The easiest way to install goleft is to download the latest binary from the releases and make sure to chmod +x the resulting binary.

If you are using go, you can build from source with: go get -u github.com/brentp/goleft/... go install github.com/brentp/goleft/cmd/goleft

goleft is also available in bioconda

Commands

  • covstats : estimate coverage and insert-size statistics on bams by sampling
  • depth : parallelize calls to samtools in user-defined windows
  • depthwed : matricize output from depth to n-sites * n-samples
  • indexcov : quick coverage estimate using only the bam index
  • indexsplit : generate regions of even data across a cohort (for parallelization)
  • samplename: report samplename(s) from a bam's SM tag

Owner

  • Name: Brent Pedersen
  • Login: brentp
  • Kind: user
  • Location: Oregon, USA

Doing genomics

GitHub Events

Total
  • Issues event: 1
  • Watch event: 4
  • Issue comment event: 1
Last Year
  • Issues event: 1
  • Watch event: 4
  • Issue comment event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 255
  • Total Committers: 6
  • Avg Commits per committer: 42.5
  • Development Distribution Score (DDS): 0.027
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Brent Pedersen b****e@g****m 248
chapmanb c****b@5****m 2
Colin Davenport c****n@h****m 2
timtribu 5****u 1
Dr. K. D. Murray 1****9 1
Aaron Quinlan a****n@g****m 1
Committer Domains (Top 20 + Academic)
50mail.com: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 68
  • Total pull requests: 11
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 3 hours
  • Total issue authors: 46
  • Total pull request authors: 7
  • Average comments per issue: 3.9
  • Average comments per pull request: 0.91
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: about 7 hours
  • Average time to close pull requests: about 4 hours
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • chapmanb (5)
  • brentp (4)
  • sjackman (3)
  • hdashnow (3)
  • lindenb (3)
  • kpalin (3)
  • andreas-wilm (2)
  • colindaven (2)
  • aofarrel (2)
  • GreeshmaThulasi (2)
  • YiweiNiu (2)
  • roblanf (2)
  • javierpradom (2)
  • martin-g (1)
  • stephenturner (1)
Pull Request Authors
  • chapmanb (4)
  • kdm9 (2)
  • brentp (2)
  • dependabot[bot] (2)
  • colindaven (1)
  • timtribu (1)
  • arq5x (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total docker downloads: 1,339
  • Total dependent packages: 2
  • Total dependent repositories: 1
  • Total versions: 30
proxy.golang.org: github.com/brentp/goleft
  • Versions: 30
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Docker Downloads: 1,339
Rankings
Docker downloads count: 1.3%
Stargazers count: 3.6%
Average: 3.6%
Dependent packages count: 4.2%
Forks count: 4.5%
Dependent repos count: 4.8%
Last synced: 6 months ago

Dependencies

go.mod go
  • git.sr.ht/~sbinet/gg v0.5.0
  • github.com/JaderDias/movingmedian v0.0.0-20220813210630-d8c6b6de8835
  • github.com/ajstarks/svgo v0.0.0-20211024235047-1546f124cd8b
  • github.com/alexflint/go-arg v1.4.3
  • github.com/alexflint/go-scalar v1.1.0
  • github.com/biogo/biogo v1.0.4
  • github.com/biogo/hts v1.4.4
  • github.com/biogo/store v0.0.0-20201120204734-aad293a2328f
  • github.com/brentp/faidx v0.0.0-20200301150453-c39eb85760d8
  • github.com/brentp/gargs v0.3.9
  • github.com/brentp/go-chartjs v0.0.0-20170901194241-a37b166b7875
  • github.com/brentp/smoove v0.2.8
  • github.com/brentp/xopen v0.0.0-20220602092336-8ece9a01569d
  • github.com/campoy/embedmd v1.0.0
  • github.com/edsrzf/mmap-go v1.0.0
  • github.com/fatih/color v1.16.0
  • github.com/go-fonts/liberation v0.3.1
  • github.com/go-latex/latex v0.0.0-20230307184459-12ec69307ad9
  • github.com/go-pdf/fpdf v0.8.0
  • github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0
  • github.com/mattn/go-colorable v0.1.13
  • github.com/mattn/go-isatty v0.0.20
  • github.com/pkg/errors v0.9.1
  • github.com/pmezard/go-difflib v1.0.0
  • go4.org v0.0.0-20230225012048-214862532bf5
  • golang.org/x/image v0.11.0
  • golang.org/x/sys v0.14.0
  • golang.org/x/text v0.12.0
  • gonum.org/v1/gonum v0.14.0
  • gonum.org/v1/plot v0.14.0
go.sum go
  • 361 dependencies