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zlib error using `@jbrowse/react-linear-genome-view` with vite

See original GitHub issue

I made a small test example of @jbrowse/react-linear-genome-vew in an app build with vite. Basically I copied over the app code from here. I had to use the solution described here to polyfill stream (for @gmod/gff) and zlib (for @gmod/cram) (I left out all the other polyfills in that example).

The app builds, but encounters an error trying to display a CRAM track:

serverSideRenderedBlock.ts:135 TypeError: Cannot read properties of undefined (reading '-5')
    at Zlib2._binding.onerror (node-modules-polyfills:zlib:357:26)
    at Zlib._error (binding.js:264:8)
    at Zlib._write (binding.js:222:10)
    at Zlib.writeSync (binding.js:171:15)
    at Gunzip.Zlib2._processChunk (node-modules-polyfills:zlib:510:31)
    at zlibBufferSync (node-modules-polyfills:zlib:229:17)
    at Object.gunzipSync (node-modules-polyfills:zlib:173:10)
    at CramFile._uncompress (file.js:247:27)
    at CramFile.readBlock (file.js:298:12)
    at async CramSlice.getBlocks (index.js:208:19)

This also could be a bug in the zlib polyfill, but I’m not really sure.

Code for a repro is here: https://codesandbox.io/s/ylt4t with the app running here: https://ylt4t.sse.codesandbox.io/.

Issue Analytics

State:
Created 2 years ago
Comments:15

Top GitHub Comments

1reaction

cmdcolincommented, Feb 18, 2022

we could possibly also improve docs related to vite in our readme’s…will consider what can be done

1reaction

cmdcolincommented, Feb 16, 2022

a new version of @gmod/cram is published (v1.6.1) that switches to pako for browser bundles, so does not require a zlib polyfill

a similar thing was also added to @gmod/bbi which also used zlib and was published as v1.0.32 so it is possible you can use the code without a zlib polyfill now, but I haven’t confirmed that

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