This PR updates the WFA2 C library to version 2.3.4. It also adds the following improvements:
implements wildcard functionality, such that mismatches where one of the sequences has a user-defined wildcard character are not penalized. This is useful for e.g. aligning sequences that have known flanks, but the middle part can vary. This is implemented using the lambda match func functionality of WFA2.
exposes linear penalty to Python
allows aligner settings to be modified after object creation
exposes max_alignment_steps option to Python
exposes indel and levenshtein distance metrics to Python
This PR updates the WFA2 C library to version 2.3.4. It also adds the following improvements: