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Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
http://martinsos.github.io/edlib
MIT License
493 stars 162 forks source link

Local Alignment? #131

Closed ayaanhossain closed 5 years ago

ayaanhossain commented 5 years ago

Is there a plan to build in local alignment (SW algorithm)? Edlib is pretty fantastic and I think having Smith-Waterman as well would make this package truly feature complete. Is there a reason, prefix and infix was baked in but not local alignment?

ayaanhossain commented 5 years ago

I don't seem to be able to change the label to "feature request" or "enhancement".

Martinsos commented 5 years ago

Hi @ayaanhossain! Unfortunately, it is impossible to support local alignment with edlib, because edlib is edit distance library, and edit distance per its definition does not play with local alignment.

I am sure however there are other libraries out there that should be a good match. I know about https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library. which is C/C++ library, but I am sure you can also find Python solutions if that is what you are looking for.

I will close the issue for now, but we can reopen it if it will be needed!