https://github.com/brentp/bcf

bcf parsing in golang
https://github.com/brentp/bcf

Last synced: 3 months ago
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bcf parsing in golang

• Host: GitHub
• URL: https://github.com/brentp/bcf
• Owner: brentp
• License: mit
• Created: 2016-12-08T22:52:38.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2016-12-09T03:53:36.000Z (about 8 years ago)
• Last Synced: 2024-09-20T00:04:14.020Z (4 months ago)
• Language: Go
• Size: 30.3 KB
• Stars: 6
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bio-go - bcf

README

        
bcf

===

[![Build Status](https://travis-ci.org/brentp/bcf.svg?branch=master)](https://travis-ci.org/brentp/bcf)

[![GoDoc] (https://godoc.org/github.com/brentp/bcf?status.png)](https://godoc.org/github.com/brentp/bcf)

`bcf` is a [bcf](https://samtools.github.io/hts-specs/BCFv2_qref.pdf) parser for the go programming language.

```Go

import "github.com/brentp/bcf"

func main() {

    rdr, _ := os.Open("some.bcf")

    brdr, _ := bcf.NewReader(rdr, 2)

    for {

        variant, err := brdr.Read()

        if err == io.EOF {

            break

        }

        fmt.Println(variant.Chrom, variant.Id, variant.Pos)

    }

}

```

TODO

====

The library is currently working, but some things remain to be done:

+ parse header into proper structure

+ fix parsing of FILTER

+ finalize parsing of FORMAT fields. This is done, but we don't currently replace the missing tokens with NaN or whatever is appropriate.

+ benchmark the current INFO and FORMAT parsing (which is lazy) that saves a slice (3 uint32's) to the underlying data to compare to just saving the offsets and having each entry in the INFO pull from

 the same underlying slice.

+ docs