@gmod/tabix

Read Tabix-indexed files using either .tbi or .csi indexes.

Install

$ npm install @gmod/tabix

Usage

Importing the module

import { TabixIndexedFile } from '@gmod/tabix'

Single file bundle

You can use tabix-js without NPM also with the tabix-bundle.js. See the example directory for usage with script tag example/index.html

<script src="https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js"></script>

TabixIndexedFile constructor

Basic usage of TabixIndexedFile under node.js supplies a path and optionally a tbiPath to the constructor. If no tbiPath is supplied, it assumes that the path+'.tbi' is the location of the tbiPath.

const tbiIndexed = new TabixIndexedFile({
  path: 'path/to/my/file.gz',
  tbiPath: 'path/to/my/file.gz.tbi',
})

You can also use CSI indexes:

const csiIndexed = new TabixIndexedFile({
  path: 'path/to/my/file.gz',
  csiPath: 'path/to/my/file.gz.csi',
})

TabixIndexedFile constructor with remote files

const remoteTbiIndexed = new TabixIndexedFile({
  url: 'http://yourhost/file.vcf.gz',
  tbiUrl: 'http://yourhost/file.vcf.gz.tbi', // can also be csiUrl
})

You can also supply a filehandle-like object from generic-filehandle2:

import { RemoteFile } from 'generic-filehandle2'

const remoteTbiIndexed = new TabixIndexedFile({
  filehandle: new RemoteFile('http://yourhost/file.vcf.gz'),
  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi'), // can also be csiFilehandle
})

getLines

The basic function this module provides is just called getLines and it returns text contents from the tabix file (it unzips the bgzipped data) and supplies it to a callback that you provide one line at a time.

Important: the start and end values that are supplied to getLines are 0-based half-open coordinates. This is different from the 1-based values that are supplied to the tabix command line tool

const lines = []
await tbiIndexed.getLines(
  'ctgA',
  200,
  300,
  function (line, fileOffset, start, end) {
    lines.push(line)
  },
)

After running this, lines contains the matching lines from the file. The callback receives:

• line — the raw line string
• fileOffset — virtual file offset, useful as a unique line identifier
• start / end — the parsed coordinates of that line (0-based half-open)

You can also pass an options object instead of a bare callback:

const lines = []
const aborter = new AbortController()
await tbiIndexed.getLines('ctgA', 200, 300, {
  lineCallback: (line, fileOffset, start, end) => lines.push(line),
  signal: aborter.signal, // an optional AbortSignal from an AbortController
})

Notes about the returned values of getLines:

• commented (meta) lines are skipped.
• line strings do not include any trailing whitespace characters.
• if getLines is called with an undefined end parameter it gets all lines from start going to the end of the contig e.g.

const lines = []
await tbiIndexed.getLines('ctgA', 0, undefined, line => lines.push(line))
console.log(lines)

API (auto-generated)

TabixIndexedFile

Table of Contents

• constructor
  • Parameters
• getLines
  • Parameters
• getHeaderBuffer
  • Parameters
• getHeader
  • Parameters
• getReferenceSequenceNames
  • Parameters
• checkLine
  • Parameters
• lineCount
  • Parameters
• readChunk
  • Parameters

constructor

Parameters

• args object
  • args.path string?
  • args.filehandle filehandle?
  • args.url string?
  • args.tbiPath string?
  • args.tbiUrl tbiUrl?
  • args.tbiFilehandle filehandle?
  • args.csiPath string?
  • args.csiUrl csiUrl?
  • args.csiFilehandle filehandle?
  • args.yieldTime number? yield to main thread after N milliseconds if reading features is taking a long time to avoid hanging main thread (optional, default 500)
  • args.renameRefSeqs function? optional function with sig string => string to 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, default n=>n)
  • args.chunkCacheSize (optional, default 5*2**20)

getLines

Parameters

• refName string name of the reference sequence
• start (number | undefined) start of the region (0-based half-open)
• end (number | undefined) end of the region (0-based half-open)
• opts (GetLinesOpts | GetLinesCallback) callback invoked for each line, or an options object with lineCallback and optional signal

Returns any promise that is resolved when the whole read is finished, rejected on error

getHeaderBuffer

get a buffer containing the "header" region of the file, which are the bytes up to the first non-meta line

Parameters

• opts Options (optional, default {})

getHeader

get a string containing the "header" region of the file, is the portion up to the first non-meta line

Parameters

• opts Options (optional, default {})

Returns Promise for a string

getReferenceSequenceNames

get an array of reference sequence names, in the order in which they occur in the file. reference sequence renaming is not applied to these names.

Parameters

• opts Options (optional, default {})

checkLine

Parameters

• metadata object metadata object from the parsed index, containing columnNumbers, metaChar, and format
• regionRefName string
• regionStart number region start coordinate (0-based-half-open)
• regionEnd number region end coordinate (0-based-half-open)
• line string

Returns object like {startCoordinate, overlaps}. overlaps is boolean, true if line is a data line that overlaps the given region

lineCount

return the number of data lines in the given reference sequence

Parameters

• refName string reference sequence name
• opts Options (optional, default {})

Returns any number of data lines present on that reference sequence

readChunk

read and uncompress the data in a chunk (composed of one or more contiguous bgzip blocks) of the file

Parameters

• c Chunk
• opts Options (optional, default {})

Publishing

Trusted publishing via GitHub Actions.

npm version patch  # or minor/major

Academic Use

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.

License

MIT © Robert Buels