Open ssnn-airr opened 8 years ago
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Cool. There are a few more implementation out there. The developers of the first one are less than responsive:
https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/issues/55
But there have been multiple versions since I last tried to install it:
Original comment by Edel Aron (Bitbucket: edel.aron, ).
I’ll definitely look into those, thanks Jason!
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Look for striped smith waterman algorithm. The problem is finding a C implementation of it with a working python wrapper that is trivial to install (via pip). See the following for a starting point:
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
I think the release this issue has sat for so long is that it’s probably a better use of time to trade out the function used for the local alignment, due to performance problems, instead of trying to hack a solution around the existing local alignment function.
Any chance that you already have some toy data to reproduce this and fix this bug?
Original report by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
When the alignment has a gap in the input sequence at the very end of the alignment, the masking is off by one. For example:
In this case,
OUTSEQ
has one extraT
. Trivial attempts to fix the problem, solve the problem in the right-hand gap case, but introduce the problem in the left-hand gap case:Will require more detailed parsing of the local alignments to fix both edge cases.