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rewrite/refactor BAM store and BAI index support into node modules #1178

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rbuels opened this Issue Aug 15, 2018 · 4 comments

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rbuels commented Aug 15, 2018

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rbuels commented Sep 4, 2018

you're going to want to use unzip from @gmod/bgzf-filehandle for unzipping the BAM chunks, I think. node zlib requires special options to properly unzip chunks that contain multiple bgzf blocks, and browserify-zlib doesn't work on them at all (devongovett/browserify-zlib#34)

const { unzip } = require('@gmod/bgzf-filehandle')
const unzipped = await unzip(chunkData)
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cmdcolin commented Sep 19, 2018

I have some progress on this on the dev...use_bamjs branch. Current concerns:

  • It is currently slower than the default implementation due to a lot of decoding of bgzip blocks, I am wondering if I might be able to optimize this
  • It requires some work on making sure the BAM features themselves are decoded properly and have a nice "feature class" and API

Nevertheless, we can view BAM files, CIGAR strings, MD tags, sequence, etc in jbrowse with the bam-js module now

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cmdcolin commented Sep 20, 2018

The speed issue is largely resolved after fixing caching layer in bam-js :)

@cmdcolin cmdcolin modified the milestones: 1.15.4, 1.15.5 Oct 5, 2018

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cmdcolin commented Oct 5, 2018

This is merged onto dev now. Please test it out with your favorite giant or weird BAM files!

@cmdcolin cmdcolin closed this Oct 5, 2018

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