tribble-index

Read htsjdk Tribble indexes (e.g. *.vcf.idx files) using pure JavaScript. Supports only Tribble version 3 linear indexes right now.

Install

$ npm install --save tribble-index

Usage

import fs from 'fs'
import read from 'tribble-index'
// or without ES6
var fs = require('fs')
var read = require('tribble-index').default.read

fs.readFile('path/to/data.vcf.idx', (err, buffer) => {
  const index = read(buffer);

  console.log(index.header)
  const blocks = index.getBlocks("ctgA",123000,456000)

  // can now use these blocks from the index to read the file
  // regions of interest
  fs.open('path/to/data.vcf', 'r', (err, fd) => {
    if (err) throw err
    blocks.forEach(({ length, offset }) => {
      const buffer = Buffer.alloc(length)
      fs.read(fd, buffer, 0, length, offset, (err, buffer) => {
        console.log('got file data', buffer)
      })
    })
    fs.close(fd, (err) => {
      if (err) throw err
    })
  })
})

API

Table of Contents

• getBlocks
• hasRefSeq
• read

getBlocks

Get an array of { offset, length } objects describing regions of the indexed file containing data for the given range.

Parameters

• refName string name of the reference sequence
• start integer start coordinate of the range of interest
• end integer end coordinate of the range of interest

hasRefSeq

Return true if the given reference sequence is present in the index, false otherwise

Parameters

• refName string

Returns boolean

read

Parse the index from the given Buffer object. The buffer must contain the entire index.

Parameters

• input Buffer

Returns (LinearIndex | IntervalTreeIndex) an index object supporting the getBlocks method

License

MIT © Robert Buels