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Smith-Waterman algorithm implementation under Apache 2 #126

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@lopozz lopozz commented Mar 6, 2025

PR for #125

Improvements from the previous version of the alignment.py:

  • improved readability of the code
  • removed global variables (match_award, mismatch_penalty, gap_penalty)
  • introduced reference to algorithm
  • apache 2.0 licence

In writing this implementation I decided to respect the signature of the original script to have a drop-in replacement for the algorithm. No additional dependencias were introduced.

The demo.py script was run successfully

Optionally I also wrote unit tests on the old script to compare it with my implementation. I could also commit those to maintain consistency in case of future PRs

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