libwfa2

Rust bindings for the wavefront algorithm (WFA2-lib, https://github.com/smarco/WFA2-lib). This is inspired by the rust crate libwfa (crate, github).

Example

Basic usage of the library.

use libwfa2::affine_wavefront::AffineWavefronts;

pub fn main() {
    let aligner = AffineWavefronts::default();

    // pattern means query
    let pattern = b"TCTTTACTCGCGCGTTGGAGAAATACAATAGT";

    // Text means reference
    let text = b"TCTATACTGCGCGTTTGGAGAAATAAAATAGT";

    aligner.align(pattern, text);

    println!("Pattern: {}", String::from_utf8_lossy(pattern));
    println!("Text:    {}\n", String::from_utf8_lossy(text));

    println!("Score: {}", aligner.score());
    println!("Cigar: {}", String::from_utf8_lossy(aligner.cigar()));
}

Setting heuristics

use libwfa2::affine_wavefront::{AffineWavefronts, HeuristicStrategy};

pub fn main() {
    println!("Example2\n");

    let mut aligner = AffineWavefronts::default();

    aligner.set_heuristic(&HeuristicStrategy::BandedStatic { band_min_k: -1, band_max_k: 1 });

    // pattern means query
    let pattern = b"TCTTTACTCGCGCGTTGGAGAAATACAATAGT";

    // Text means reference
    let text = b"TCTATACTGCGCGTTTGGAGAAATAAAATAGT";

    let _status = aligner.align(pattern, text);

    println!("Pattern: {}", String::from_utf8_lossy(pattern));
    println!("Text:    {}\n", String::from_utf8_lossy(text));

    println!("Score: {}", aligner.score());
    println!("Cigar: {}", String::from_utf8_lossy(aligner.cigar()));
}