I see this is only done for the target sequence. We should consider doing it for both because the mashmap breakpoints may not be precise.
However, we might also want to disable it altogether so that the alignments really are on the mapped range, so that we don't get any edge effects and the alignment boundaries can be respected.
I see this is only done for the target sequence. We should consider doing it for both because the mashmap breakpoints may not be precise.
However, we might also want to disable it altogether so that the alignments really are on the mapped range, so that we don't get any edge effects and the alignment boundaries can be respected.