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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Overlap primary mapping #58

Open biomichal opened 5 years ago

biomichal commented 5 years ago

Hi philres, I wonder whether NGLMR have multiple mapping fragments for a reads in the primary mapping records? I don't mean the secondary alignments. For example, for a split mapping of a reads, is there the cases the 1-5000 bp align to one position, and the other 3000-10000 bp align to another position in reference? I did not test, just for curious. Thank you.

fritzsedlazeck commented 5 years ago

One of them should be marked as primary and one as secondary alignment. I hope that helps. Cheers Fritz