bíogo/hts

bíogo/hts: high throughput sequence handling for the Go language - Published in JOSS (2017)

https://github.com/biogo/hts

Science Score: 95.0%

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
Found .zenodo.json file
✓
DOI references
Found 5 DOI reference(s) in README and JOSS metadata
○
Academic publication links
✓
Committers with academic emails
1 of 9 committers (11.1%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Last synced: 4 months ago · JSON representation

Repository

biogo high throughput sequencing repository

Basic Info

Host: GitHub
Owner: biogo
License: bsd-3-clause
Language: Go
Default Branch: master
Homepage:
Size: 1.22 MB

Statistics

Stars: 128
Watchers: 9
Forks: 41
Open Issues: 7
Releases: 1

Created almost 11 years ago · Last pushed over 1 year ago

Metadata Files

Readme Contributing Funding License Codemeta

HTS

Installation

    $ go get github.com/biogo/hts/...

Overview

SAM and BAM handling for the Go language.

bíogo/hts provides a Go native implementation of the SAM specification for SAM and BAM alignment formats commonly used for representation of high throughput genomic data, the BAI, CSI and tabix indexing formats, and the BGZF blocked compression format. The bíogo/hts packages perform parallelized read and write operations and are able to cache recent reads according to user-specified caching methods. The bíogo/hts APIs have been constructed to provide a consistent interface to sequence alignment data and the underlying compression system in order to aid ease of use and tool development.

Example usage

The following code implements the equivalent of samtools view -c -f n -F N file.bam.

``` package main

import ( "flag" "fmt" "io" "log" "os"

"github.com/biogo/hts/bam"
"github.com/biogo/hts/bgzf"
"github.com/biogo/hts/sam"

)

var ( require = flag.Int("f", 0, "required flags") exclude = flag.Int("F", 0, "excluded flags") file = flag.String("file", "", "input file (empty for stdin)") conc = flag.Int("threads", 0, "number of threads to use (0 = auto)") help = flag.Bool("help", false, "display help") )

const maxFlag = int(^sam.Flags(0))

func main() { flag.Parse() if *help { flag.Usage() os.Exit(0) }

if *require > maxFlag {
    flag.Usage()
    log.Fatal("required flags (f) out of range")
}
reqFlag := sam.Flags(*require)

if *exclude > maxFlag {
    flag.Usage()
    log.Fatal("excluded flags (F) out of range")
}
excFlag := sam.Flags(*exclude)

var r io.Reader
if *file == "" {
    r = os.Stdin
} else {
    f, err := os.Open(*file)
    if err != nil {
        log.Fatalf("could not open file %q:", err)
    }
    defer f.Close()
    ok, err := bgzf.HasEOF(f)
    if err != nil {
        log.Fatalf("could not open file %q:", err)
    }
    if !ok {
        log.Printf("file %q has no bgzf magic block: may be truncated", *file)
    }
    r = f
}

b, err := bam.NewReader(r, *conc)
if err != nil {
    log.Fatalf("could not read bam:", err)
}
defer b.Close()

// We only need flags, so skip variable length data.
b.Omit(bam.AllVariableLengthData)

var n int
for {
    rec, err := b.Read()
    if err == io.EOF {
        break
    }
    if err != nil {
        log.Fatalf("error reading bam: %v", err)
    }
    if rec.Flags&reqFlag == reqFlag && rec.Flags&excFlag == 0 {
        n++
    }
}

fmt.Println(n)

} ```

Getting help

Help or similar requests are preferred on the biogo-user Google Group.

https://groups.google.com/forum/#!forum/biogo-user

Contributing

If you find any bugs, feel free to file an issue on the github issue tracker. Pull requests are welcome, though if they involve changes to API or addition of features, please first open a discussion at the biogo-dev Google Group.

https://groups.google.com/forum/#!forum/biogo-dev

Citing

If you use bíogo/hts, please cite Kortschak, Pedersen and Adelson "bíogo/hts: high throughput sequence handling for the Go language", doi:10.21105/joss.00168.

Library Structure and Coding Style

The coding style should be aligned with normal Go idioms as represented in the Go core libraries.

Copyright and License

BITSTREAM CHARTER is a registered trademark of Bitstream Inc.

Owner

Name: bíogo
Login: biogo
Kind: organization

Repositories: 14
Profile: https://github.com/biogo

bíogo is a bioinformatics library collection for Go

JOSS Publication

bíogo/hts: high throughput sequence handling for the Go language

Published

February 04, 2017

DOI

10.21105/joss.00168

Volume 2, Issue 10, Page 168

Authors

R Daniel Kortschak

School of Biological Sciences, The University of Adelaide

Brent S. Pedersen

Department of Human Genetics, University of Utah

David L. Adelson

School of Biological Sciences, The University of Adelaide

Editor

Pjotr Prins

CodeMeta (codemeta.json)

{
  "@context": "https://raw.githubusercontent.com/mbjones/codemeta/master/codemeta.jsonld",
  "@type": "Code",
  "author": [
    {
      "@id": "http://orcid.org/0000-0001-8295-2301",
      "@type": "Person",
      "email": "dan.kortschak@adelaide.edu.au",
      "name": "R Daniel Kortschak",
      "affiliation": "School of Biological Sciences, The University of Adelaide"
    },
    {
      "@id": "https://orcid.org/0000-0003-1786-2216",
      "@type": "Person",
      "email": "brentp@genetics.utah.edu",
      "name": "Brent S Pedersen",
      "affiliation": "Department of Human Genetics, University of Utah"
    },
    {
      "@id": "http://orcid.org/0000-0003-2404-5636",
      "@type": "Person",
      "email": "david.adelson@adelaide.edu.au",
      "name": "David L Adelson",
      "affiliation": "School of Biological Sciences, The University of Adelaide"
    }
  ],
  "identifier": "",
  "codeRepository": "https://github.com/biogo/hts",
  "datePublished": "2017-01-06",
  "dateModified": "2017-02-01",
  "dateCreated": "2017-01-06",
  "description": "high throughput sequence handling for the Go language",
  "keywords": "bioinformatics, high throughput sequencing, golang",
  "license": "BSD-3 like",
  "title": "bíogo/hts",
  "version": "v1.0.1"
}

GitHub Events

Total

Watch event: 2
Issue comment event: 1
Fork event: 1

Last Year

Watch event: 2
Issue comment event: 1
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 456
Total Committers: 9
Avg Commits per committer: 50.667
Development Distribution Score (DDS): 0.064

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
kortschak	d**k@a**u	427
Brent Pedersen	b**e@g**m	17
Egon Elbre	e**e@g**m	5
Yaz Saito	y**o@g**m	2
Wei Xu	x**7@g**m	1
Shengjing Zhu	z**j@d**g	1
Clayton Wheeler	c**r@g**m	1
Brennon Loveless	b**s@g**m	1
Jason Travis	j**s@t**g	1

Committer Domains (Top 20 + Academic)

tgen.org: 1 genomenon.com: 1 debian.org: 1 grailbio.com: 1 adelaide.edu.au: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 34
Total pull requests: 71
Average time to close issues: 2 months
Average time to close pull requests: 20 days
Total issue authors: 16
Total pull request authors: 12
Average comments per issue: 4.97
Average comments per pull request: 1.34
Merged pull requests: 61
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

brentp (9)
kortschak (6)
dongweigogo (3)
bloveless (2)
yipal (2)
bsipos (2)
ZhongbaoShi (1)
mnsmar (1)
sb10 (1)
ns3116 (1)
seqyuan (1)
jpofmars (1)
chrchang (1)
nathanhaigh (1)
defgenx (1)

Pull Request Authors

kortschak (49)
brentp (8)
yasushi-saito (4)
xuweixw (2)
bsipos (2)
bloveless (2)
zhsj (1)
yipal (1)
ckingsford (1)
egonelbre (1)
AlanRace (1)
csw (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads: unknown
Total docker downloads: 15,067,665

Total dependent packages: 96
Total dependent repositories: 162
Total versions: 14

proxy.golang.org: github.com/biogo/hts

Homepage: https://github.com/biogo/hts
Documentation: https://pkg.go.dev/github.com/biogo/hts#section-documentation
License: BSD-3-Clause
Latest release: v1.4.5
published over 1 year ago

Versions: 14
Dependent Packages: 96
Dependent Repositories: 162
Docker Downloads: 15,067,665

Rankings

Docker downloads count: 0.4%

Dependent repos count: 0.5%

Dependent packages count: 0.5%

Average: 2.0%

Forks count: 4.0%

Stargazers count: 4.5%

Last synced: 4 months ago

Dependencies

go.mod go

github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1
github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560
github.com/kr/pretty v0.2.0
github.com/ulikunitz/xz v0.5.10
gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15

go.sum go

github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1
github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560
github.com/kr/pretty v0.2.0
github.com/kr/pty v1.1.1
github.com/kr/text v0.1.0
github.com/ulikunitz/xz v0.5.10
gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15

bíogo/hts

Science Score: 95.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

HTS

Installation

Overview

Example usage

Getting help

Contributing

Citing

Library Structure and Coding Style

Copyright and License

Owner

JOSS Publication

bíogo/hts: high throughput sequence handling for the Go language

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/biogo/hts

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Dependencies