Error while parsing a custom-format bigbed file

[azangru]

Hi,

I am getting an error when trying to parse a custom bigbed file that contains 21 columns (bed4+17). I am running bbi-js thus:

import  { BigBed } from '@gmod/bbi';
import { LocalFile } from 'generic-filehandle';

const test = async () => {
  try {
    const file = new BigBed({
      filehandle: new LocalFile(require.resolve('<path-to-the-bigbed-file>')),
    });
    const { autoSql } = await file.getHeader(); // <-- this errors
  } catch (error) {
    console.log('error', error);
  }
};

The error message is: RangeError: Offset is outside the bounds of the DataView

I could trace the code execution down to this line in bbi.ts

bbi-js/src/bbi.ts

Line 202 in ee02414

const sum = ret.totalSummaryParser.parse(tail)

but then it calls the binary parser, at which point I get lost.

I am providing the problematic bigbed, as well as the source files from which the bigbed was generated. I am not sure whether the problem is with the bigbed file itself or with the bbi-js library; but would like to point out that the bigbed file can be parsed back into bed by the bigbedToBed tool, and can also be read by the pyBigWig python library.

Attachments:

• bigbed.zip — the bigbed that causes the error
• input.zip — an archived directory with source files from which the bigbed was generated by running the command bedToBigBed -as=transcripts.as -type=bed4+17 transcripts.bed chrom.sizes transcripts.bb

[cmdcolin]

@azangru thanks much for the detailed issue report. I came up with a improved fix here #57

I can probably create a quick bugfix release for it :)

[cmdcolin]

published fix as 4.0.2! the pr autoclosed this but let me know if that helps

[azangru]

@cmdcolin thank you so much such a quick response! I am happy to report that 4.0.2 fixes the issue for me.

BTW, while checking that the fix works, I noticed a couple of typos in a code snippet in the readme:

There's a closing backtick missing (first red arrow), and a backslash where it shouldn't be (second red arrow).

[cmdcolin]

excellent, glad that worked. that syntax should be fixed in the github readme now too