@gmod/bgzf-filehandle
v2.0.4
Published
read from a compressed bgzip file (with .gzi) as if it were uncompressed
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Readme
Transparently read indexed block-gzipped (BGZF) files, such as those created by bgzip, using coordinates from the uncompressed file. The module is used in @gmod/indexedfasta to read bgzip-indexed fasta files (with gzi index, fai index, and fa).
Users can also use the unzip
function to unzip bgzip files whole (which pako
has trouble with natively)
You can also use the unzipChunkSlice function to unzip ranges given by BAI or TBI files for BAM or tabix file formats (which are bgzip based).
The unzip
utility function properly decompresses BGZF chunks in both node and
the browser, using pako
when running in the browser and native zlib
when
running in node.
Install
$ npm install --save @gmod/bgzf-filehandle
Usage
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.
License
MIT © Robert Buels