https://github.com/brentp/bix

tabix file access with golang using biogo machinery
https://github.com/brentp/bix

Last synced: 4 months ago
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tabix file access with golang using biogo machinery

• Host: GitHub
• URL: https://github.com/brentp/bix
• Owner: brentp
• License: mit
• Created: 2015-09-04T17:17:26.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2019-07-18T14:09:52.000Z (almost 6 years ago)
• Last Synced: 2025-02-02T04:41:11.322Z (5 months ago)
• Language: Go
• Size: 477 KB
• Stars: 10
• Watchers: 4
• Forks: 15
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
bix

===

Tabix files in go.

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

`Bix`is a pure go tabix reader. Tabix has a minimum resolution of 16K bases. So, for dense annotations

like ExAC, repeated queries will have to re-parse the same intervals. To mitigate this, `Bix` caches

all annotations for the blocks from each query and re-uses them for later querires to the same block.

In practice, this results in 10X-100X speedup for any type of data.

```go

tbx, err := bix.New(f)

// Query returns an io.Reader

ph := true // print header ?

rdr, err := tbx.Query(chrom, start, end, ph)

buf := bufio.NewReader(rdr)

for {

	line, err := bufr.ReadString('\n')

	if err == io.EOF {

		break

	}

	fmt.Println(line)

}

// or

intervals := tbx.Get(chrom, start, end)

```

where intervals will be either a vcfgo.Variant or an Interval object with a Chrom(), Start(), and End() method.