Incorrect soft clipped region after insertion (one off error?)

[Maarten-vd-Sande]

Describe the bug

I have two reads in the same region. They both have the same last 9 nucleotides, and they are soft-clipped. One of the two has an insertion earlier in the sequence. This is how jbrowse shows them:

When I show soft-clipped nucleotides, it shows 9 nucleotides for both reads. Yet, the soft-clipped sequences are identical in the bam file, but I think jbrowse2 introduces a one-off error here by duplicating the last C nucleotide:

I think it has to do with the fact that one of the two sequences has an insertion earlier.

To Reproduce

This is the config, reference genome and bam file:

example.zip

It contains only one contig. To see the effect the clearest you will have to color per nucleotide, and show soft clipping. When you click on the two reads, you can see that the last 9 nucleotides are identical between them.

Version:

2.10.2 browser version (firefox)

Additional context

[cmdcolin]

thanks for reporting this. I can confirm and it affects both bam and cram. will try to whip up a fix

[Maarten-vd-Sande]

Thanks for fixing this! Awesome! 😄