BAM record is not updated properly for reverse orientation transcripts

OceanGenomics / mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates

BSD 3-Clause "New" or "Revised" License

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BAM record is not updated properly for reverse orientation transcripts #14

Closed haghshenas closed 2 years ago

haghshenas commented 2 years ago

If an alignment is being projected to a transcript that is on the reverse strand, then CIGAR, sequence and quality should be reversed (or reverse complemented).