Function parasailors::local_alignment_score

pub fn local_alignment_score(query_profile: &Profile, database_sequence: &[u8], open_cost: i32, gap_extend_cost: i32) -> i32

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

Examples

let query = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTNNNNNNNNN";
let profile_ident = Profile::new(query, &identity_matrix);

let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTNNNNNNNNN";
assert_eq!(50, local_alignment_score(&profile_ident, reference, 1, 1));

let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTCCTTTTTTNNNNNNNNN";
assert_eq!(48, local_alignment_score(&profile_ident, reference, 1, 1));

let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTT";
assert_eq!(35, local_alignment_score(&profile_ident, reference, 1, 1));