Function parasailors::local_alignment_score_no_profile

pub fn local_alignment_score_no_profile(
    query: &[u8], 
    database_sequence: &[u8], 
    open_cost: i32, 
    gap_extend_cost: i32, 
    sub_matrix: &Matrix
) -> i32

Returns a score for local pairwise alignment using a vectorized version of Smith-Waterman.

Examples

let identity_matrix = Matrix::new(MatrixType::Identity);
let query = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTNNNNNNNNN";

let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTNNNNNNNNN";
assert_eq!(50, local_alignment_score_no_profile(query, reference, 1, 1, &identity_matrix));

let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTCCTTTTTTNNNNNNNNN";
assert_eq!(48, local_alignment_score_no_profile(query, reference, 1, 1, &identity_matrix));

let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTT";
assert_eq!(35, local_alignment_score_no_profile(query, reference, 1, 1, &identity_matrix));