Intermittent Error "Cannot read properties of null (reading 'length')" when loading CRAM tracks

[atruji]

Hi, Our team is encountering a "Cannot read properties of null (reading 'length')" Error when trying to load and view CRAM data tracks. When controlling for data file and region the error only occurs on some attempts. Providing a pause by adding a breakpoint during runtime at the line that returns the error allows the track data to load successfully. The line in app_bundle-1.13.6.js is 36870 (code block below) and we are using igv-webapp.2.13.5.

if (t.length !== e.refSeqSpan) throw new o.CramArgumentError("seqFetch callback returned a reference sequence of the wrong length"); return { seq: t, start: e.refSeqStart, end: e.refSeqStart + e.refSeqSpan - 1, span: e.refSeqSpan

[jrobinso]

Apologies for the delayed response. Without a test case to reproduce this it will be difficult to address. Are you seeing this with multiple CRAM files?

@cmdcolin it looks like the error is here, starting at line 326 of cramFile/slice/index.ts. Its definitely not expecting "null" for seq, and even if it checked for null it would still need to throw an error.

      if (seq.length !== sliceHeader.refSeqSpan) {
        throw new CramArgumentError(
          'seqFetch callback returned a reference sequence of the wrong length',
        )
      }

[cmdcolin]

could be worth checking the code for the "seqFetcher" that is passed to the CRAM library constructor to see whether there would be any case that it returns null

[jrobinso]

@cmdcolin Ah yes, good point, that's where the problem is.

[jrobinso]

@atruji If you can come up with a repeatable test case please post instructions here.

[jrobinso]

Also, when this happens are there any errors in the console? You can access the console from "View > Developer > Developer Tools" on Chrome. Most other browsers also have some form of developer tools.