Open PeteHaitch opened 9 years ago
I don't have any --pbat
or --non_directional
libraries with which to test. However, I think this will cause problems with methtuple
. Specifically, read-1 when mapped to CTOT or CTOB has the "second in pair" flag set when it is really the first in the pair. SImilarly, read-2 when mapped to CTOT or CTOB has the "first in pair" flag set when it is really the second in the pair. So this change seems like a workaround in order to get Seqmonk to display things in a desired way, but it also breaks the meaning of the flags according to the SAM specifications. Have raised with Felix https://github.com/FelixKrueger/Bismark/issues/41
From http://www.bioinformatics.babraham.ac.uk/projects/bismark/RELEASE_NOTES.txt: