bam-best runs on BAMs without @RG readgroups, but fails at the end and truncates them

[AndrewC160]

If the BAM files used do not contain an @ RG header, bam-best appears to finish the file fine but then fail at 100%, truncating the output BAMs and failing to produce a stats file. Not a tremendous issue since most BAMs will have @ RG headers and easy enough to fix, but maybe it would be possible to use a dummy @ RG value with a warning, or just have bam-best check for this at run time.

The essential part of the error message with such files is the following:

Cannot invoke htsjdk.samtools.SAMRecord.getReadName() because buffer[idx] is null

[mbreese]

Can you include a full stack trace? I can't find where read-groups would play into this...

I think you are seeing two separate issues.

The other thing to try is to run bam-best with the -v verbose argument to see exactly what read throws the error.