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update WFA2-lib, expose more options to Python #13

Merged
merged 11 commits into from
Feb 27, 2024
Merged

update WFA2-lib, expose more options to Python #13

merged 11 commits into from
Feb 27, 2024

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ilia-kats
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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

@kcleal
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kcleal commented Feb 27, 2024

Thanks @ilia-kats, This looks like a lot of work! Cheers

@kcleal kcleal merged commit 734c970 into kcleal:master Feb 27, 2024
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2 participants