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Daniel-Liu-c0deb0t / triple_accel

Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.
MIT License
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Traceback inaccurate with gap open costs #9

Open Daniel-Liu-c0deb0t opened 2 years ago

Daniel-Liu-c0deb0t commented 2 years ago

Need to keep track of traceback for the gap matrices (whether continuing or opening a gap). Currently, following gap transitions just end up on an entry in the dp matrix (not the gap matrices) even if its continuing a gap.

RagnarGrootKoerkamp commented 1 year ago

As an example, when aligning AC and AACC with cost model (sub=1, open=1, extend=1), triple_accel correctly returns cost 3, but the cigar is X=X= instead of =XX=.