Read htsjdk Tribble indexes (e.g. *.vcf.idx files) using pure JavaScript. Supports only Tribble version 3 linear indexes right now.
$ npm install --save @gmod/tribble-index
import TribbleIndexedFile from '@gmod/tribble-index'
// or without ES6
const { TribbleIndexedFile } = require('@gmod/tribble-index')
const indexedFile = new TribbleIndexedFile({ path: 'path/to/data.vcf' })
// by default, assumes tribble index at path/to/data.vcf.idx
// can also provide `tribblePath` if the tribble is named differently
async function doStuff() {
// iterate over lines in the specified region, each of which
// is structured as
const lines = []
await indexedFile.getLines('contigA', 3000, 3200, line => lines.push(line))
// lines is now an array of strings, which are data lines.
// commented (meta) lines are skipped.
// line strings do not include any trailing whitespace characters.
console.log(lines)
// ↳ [ 'contigA\t3000\trs17883296\tG\tT\t100\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:AP\t0|0:0.000,0.000']
// get the approximate number of data lines in the file for the
// given reference sequence, excluding header, comment, and whitespace lines
console.log(await indexedFile.lineCount('contigA'))
// ↳ 109
// get the "header text" string from the file, which is the first contiguous
// set of lines in the file that all start with a "meta" character (usually #)
console.log(await indexedFile.getHeader())
// ↳ ##fileformat=VCFv4.1
// ↳ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
// or if you want a buffer instead, there is getHeaderBuffer()
console.log(await indexedFile.getHeaderBuffer())
// ↳ <Buffer 23 23 66 69 6c 65 66 6f 72 6d 61 74 3d 56 43 46 76 34 2e 31 0a 23 23 66 69 6c 65 ... >
}Also supports a lower-level interface
import fs from 'fs'
import read from '@gmod/tribble-index'
// or without ES6
const fs = require('fs')
const read = require('@gmod/tribble-index')
fs.readFile('path/to/data.vcf.idx', (err, buffer) => {
if (err) throw err
const index = read(buffer)
console.log(index)
const blocks = index.getBlocks('contigA', 3000, 3200)
// can now use these blocks from the index to read the file
// regions of interest
fs.open('path/to/data.vcf', 'r', (err2, fd) => {
if (err2) throw err2
blocks.forEach(({ length, offset }) => {
const buffer2 = Buffer.alloc(length)
fs.read(fd, buffer2, 0, length, offset, (err3, bytesRead, buffer3) => {
if (err3) throw err3
console.log('got file data', buffer3)
})
})
fs.close(fd, err4 => {
if (err4) throw err4
})
})
})- getBlocks
- getMetadata
- hasRefSeq
- read
- constructor
- checkLine
- getReferenceSequenceNames
- getHeaderBuffer
- getHeader
- lineCount
Get an array of { offset, length } objects describing regions of the indexed file containing data for the given range.
refNamestring name of the reference sequencestartinteger start coordinate of the range of interestendinteger end coordinate of the range of interest
Returns an object like { fileMD5 fileName fileSize fileTimestamp firstDataOffset flags magic properties type version chromosomes}
Return true if the given reference sequence is present in the index, false otherwise
refNamestring
Returns boolean
Parse the index from the given Buffer object. The buffer must contain the entire index.
inputBuffer
Returns (LinearIndex | IntervalTreeIndex) an index object supporting the getBlocks method
argsobjectargs.pathstring?args.filehandlefilehandle?args.tribblePathstring?args.tribbleFilehandlefilehandle?args.metaCharstring? character that denotes the beginning of a header line (optional, default'#')args.columnNumbersobject? object like {ref start end} defining the (1-based) columns in the file. end may be set to -1 if not present. default {ref: 1, start: 2, end: -1} (optional, default{ref:1,start:2,end:-1})args.oneBasedClosedboolean? whether the indexed file uses one-based closed coordinates. default false (implying zero-based half-open coordinates) (optional, defaultfalse)args.chunkSizeLimitnumber? maximum number of bytes to fetch in a singlegetLinescall. default 2MiB (optional, default2000000)args.yieldLimitnumber? maximum number of lines to parse without yielding. this avoids having a large read prevent any other work getting done on the thread. default 300 lines. (optional, default300)args.renameRefSeqsfunction? optional function with sigstring => stringto transform reference sequence names for the purpose of indexing and querying. note that the data that is returned is not altered, just the names of the reference sequences that are used for querying. (optional, defaultn=>n)args.blockCacheSizenumber? maximum size in bytes of the block cache. default 5MB (optional, default5*2**20)
regionRefNamestringregionStartnumber region start coordinate (0-based-half-open)regionEndnumber region end coordinate (0-based-half-open)line
Returns object like {startCoordinate, overlaps}. overlaps is boolean,
true if line is a data line that overlaps the given region
get an array of reference sequence names
reference sequence renaming is not applied to these names.
Returns Promise for an array of string sequence names
get a buffer containing the "header" region of the file, which are the bytes up to the first non-meta line
Returns Promise for a buffer
get a string containing the "header" region of the file, is the portion up to the first non-meta line
Returns Promise for a string
return the approximate number of data lines in the given reference sequence returns -1 if the reference sequence is not found
refSeqstring reference sequence name
Returns Promise for number of data lines present on that reference sequence
This package was written with funding from the NHGRI as part of the JBrowse project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from jbrowse.org.
MIT © Robert Buels