Closed donkirkby closed 7 years ago
Hi @donkirkby,
Thanks so much for reporting this bug and providing a minimal case to reproduce. I ran your script on the current master
branch and could not reproduce the bug, and I think it is related to #6:
is2882:tests art$ python issue12.py
True
-495
True
-45
Could you please pull and try again?
Yes, it works for me now. Closing the issue.
I would expect that it should always be able to align one string against its substring. Even weirder, it's successful against a longer string.
Here's a script to reproduce the failure:
Results:
This reference is part of HIV1-C-BR-JX140663 that we've been using to map reads for our G2P algorithm. Related to this: the other Gotoh library we use doesn't seem to penalize big gaps at the end. I don't know if that's a problem or not.