This is python + rust bindings of a Striped Smith Waterman algorithm.
It is a reimplementation of this library: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/ using rust.
It takes about 2x the amount of time as the C implementation takes to run, but it is not built for speed, it is built to mirror the C implementation as closely as possible. I'm interested in optimizing the code, but I'm not actively working on that.
SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
Please note that changes to the underlying rust library should be done against src/rust/dpf-ssw-aligner-rs/src/lib.rs as
this library only implements the python wrapping part. I just copy that file into this folder and rename it.
TODO
License: MIT
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