Fix for rendering of softclipping when there are insertions in the sequence #4402
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cmdcolin
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Fixes #4401
The code now processes the entire CIGAR string to get the seqOffset and refOffset. This is canonical CIGAR parsing code that is pretty idiomatic. The alternative to this would be adding an extra field for seqOffset to the mismatches datastructure. possibly that could be considered later on, but it would actually increase memory consumption so it's a tradeoff
this branch, showing both BAM and CRAM softclipping on long reads that have insertions and deletions. this actually looks expected as it shows that the alignments are pretty similar nearby the clip site but then diverge as they move away from it (compared to main branch, where it is almost random)
main branch, showing both BAM and CRAM softclipping on long reads that have insertions and deletions
