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torognes / swipe

Smith-Waterman database searches with inter-sequence SIMD parallelisation
GNU Affero General Public License v3.0
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Show all descriptions and alignments with maximum score #38

Open krdav opened 1 year ago

krdav commented 1 year ago

Clunky way of solving the request that I wrote about in this issue: https://github.com/torognes/swipe/issues/37

Not suggesting this as the actual solution, but rather showing it so that it is clear what I am referring to in the issue. In a better solution the show_best option should probably be a boolean or yes/no and there is probably a more intelligent way of implementing it such that showhits and showalignments are not forced to be the same.

krdav commented 1 year ago

Update: Instead of showing only top scoring sequences, I changed it such that it allows showing multiple levels e.g.
show_best=1 shows sequences with the highest score
show_best=2 shows sequences with the highest and second highest score
etc

torognes commented 1 year ago

Thanks for the suggested change to swipe. I haven't worked on the swipe code for a long time, but will try to find time to look at this soon.

krdav commented 1 year ago

Thank you so much! I understand if you got other priorities, not working on the swipe code. But Swipe just happen to be very fast - in my experience a lot faster than other SW tools/libraries.