Properly set the flag for secondary alignments

OceanGenomics / mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates

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

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Properly set the flag for secondary alignments #13

Open haghshenas opened 2 years ago

gmarcais commented 2 years ago

@haghshenas Would you care to provide a few more details on that bug?

gmarcais commented 2 years ago

Didn't mean to close. Fat finger goof up.

haghshenas commented 2 years ago

Hi Guillaume, Hope you are doing well.

Based on SAM specifications, if a read has multiple alignments, only one alignment should be considered primary. All other alignments should have the secondary alignment flag set. I opened this issue as a reminder that at that time mudskipper was not following this standard, specifically for genes with multiple transcripts.

gmarcais commented 2 years ago

Thanks for the quick answer Ehsan.