read from a compressed bgzip file (with .gzi) as if it were uncompressed


4101.4.024 days ago3 years agoMinified + gzip package size for @gmod/bgzf-filehandle in KB


NPM version Build Status Greenkeeper badge codecov

Transparently read indexed block-gzipped (BGZF) files, such as those created by bgzip, using coordinates from the uncompressed file.

Also provides a unzip utility function that properly decompresses BGZF chunks in both node and the browser. Uses pako when running in the browser, native zlib when running in node. The unzipChunk function is another


$ npm install --save @gmod/bgzf-filehandle


const { BgzfFilehandle, unzip, unzipChunk } = require('@gmod/bgzf-filehandle')

const f = new BgzfFilehandle({path: 'path/to/my_file.gz'})
// assumes a .gzi index exists at path/to/my_file.gz.gzi. can also
// pass `gziPath` to set it explicitly. Can also pass filehandles
// for the files: `filehandle` and `gziFilehandle`

// supports a subset of the NodeJS v10 filehandle API. currently
// just read() and stat()
const myBuf = Buffer.alloc(300)
await f.read(myBuf, 0, 300, 23234)
// now use the data in the buffer

const { size } = f.stat() // stat gives the size as if the file were uncompressed

// unzip takes a buffer and returns a promise for a new buffer
const chunkDataBuffer = readDirectlyFromFile(someFile, 123, 456)
const unzippedBuffer = await unzip(chunkDataBuffer)

// unzipChunk takes a buffer and returns a decompressed buffer plus the offsets
// of the block boundaries in the bgzip file in compressed (cpositions) and
// decompressed (dpositions) coordinates
// you can ignore dpositions/cpositions if your code doesn't care about stable feature IDs
const {buffer, dpositions, cpositions} = await unzipChunk(chunkDataBuffer)

// similar to the above unzipChunk but takes extra chunk argument and trims
// off (0,chunk.minv.dataPosition) and (chunk.maxv.dataPosition)
// used especially for generating stable feature IDs across chunk boundaries
// normal unzip or unzipChunk can be used if this is not important
const {buffer, dpositions, cpositions} = await unzipChunkSlice(chunkDataBuffer, chunk)

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.


MIT © Robert Buels

If you find any bugs or have a feature request, please open an issue on github!

The npm package download data comes from npm's download counts api and package details come from npms.io.