Is there a way to report all alignments up to the distance requested? For example if I have an alignment with distance of 1 in the beginning of a query I might prefer that to an alignment with distance of 0 somewhere else.
The solution I can think of is to have a moving window across the query; however, I believe these suboptimal alignments are already found but just not reported. Something like this would be very useful for trimming trailing or leading strings from a longer one.
Is there a way to report all alignments up to the distance requested? For example if I have an alignment with distance of 1 in the beginning of a query I might prefer that to an alignment with distance of 0 somewhere else.
The solution I can think of is to have a moving window across the query; however, I believe these suboptimal alignments are already found but just not reported. Something like this would be very useful for trimming trailing or leading strings from a longer one.