Support for CIGAR strings containing X and = ops

[mbabadi]

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.

[emi80]

Hi @mbabadi,
thanks for reporting this. We will definitely have a look at these CIGAR ops and let you know.

Best,
Emilio