Open msto opened 7 months ago
We use the SetMateInfoIterator
from htsjdk which routes to the setMateInformationOnSupplementalAlignment
method
It looks like MQ is not set on the supplementary records, so we'd likely need to make a PR into htsjdk, wait for a release, then update fgbio's htsjdk dependency.
Currently,
SetMateInformation
does not add theMQ
tag to supplementary alignments.I'm not sure if this is intended behavior - the docs suggest that supplementary alignments would have this tag added.
GroupReadsByUmi
requires that all alignments, including supplementary alignments, have theMQ
tag set, so it would be helpful ifSetMateInformation
produced a compatible BAM 🙂