There are two mapper-related distmap arguments that should be conditional on the mapper used (error if provided without the mapper, and required/optional depending on the argument):
[ ] --gsnap-output-split - I know very little about this
[ ] bwa-sampe-args - should be used for bwa-aln, and it might be required to be sure that it is doing what the user expects
There are two mapper-related distmap arguments that should be conditional on the mapper used (error if provided without the mapper, and required/optional depending on the argument):
--gsnap-output-split- I know very little about thisbwa-sampe-args- should be used for bwa-aln, and it might be required to be sure that it is doing what the user expects