Repository navigation
Support for CIGAR strings containing X and = ops #71
Description
New feature
Add support for CIGAR strings containing X and =. These are allowed in SAM specs v1.4, though, ggsashimi neglects all such reads.
Usage scenario
It is not uncommon to come across .bam files that containg X and = ops in the CIGAR strings. For instance, running minimap2 with --eqx arguments generates such cigar strings. In such cases, ggsashimi throws away all alignments and produces an empty plot without producing an informative error message.
Suggest implementation
As a simple implementation, one can replace all X and = with M and merge tandem M ops if needed. I have tried this workaround and it works well.
Activity
emi80 commentedon Sep 8, 2021
Hi @mbabadi,
thanks for reporting this. We will definitely have a look at these CIGAR ops and let you know.
Best,
Emilio