how can I avoid doing reverse complement alignments?

mengyao / Complete-Striped-Smith-Waterman-Library

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how can I avoid doing reverse complement alignments? #57

Closed juancresc closed 2 years ago

juancresc commented 6 years ago

I need to do only + strand alignments (I need to align a sequence against its reverse complement) so i would use the same string, but if I do so, I'll always get a full alignment. Any ideas?