Function rust_spoa::poa_consensus

pub fn poa_consensus(
    seqs: &Vec<Vec<u8>>, 
    consensus_max_length: usize, 
    alignment_type: i32, 
    match_score: i32, 
    mismatch_score: i32, 
    gap_open: i32, 
    gap_extend: i32
) -> Vec<u8>

Generates a consensus sequence from a list of sequences.

Arguments

• seqs - a vector holding the sequences (each as a null-terminated vector of u8) to form a consensus from
• consensus_max_len - The upper bound for the output consensus length. If the output consensus sequence is longer than this value, it will be truncated to this length. Setting a large value uses more memory and runtime, since a buffer of this size is allocated internally.
• alignment_type - alignment mode: 0 = local, 1 = global, 2 = gapped
• match_score - the match score for alignment
• mismatch_score - the mismatch score for alignment
• gap_open - the gap open score for alignment
• gap_extend - the gap extend score for alignment

Returns

• returns the consensus of the input sequences as a vector of u8

Examples

    use rust_spoa::poa_consensus;

    fn test_dna_consensus() {
       let mut seqs = vec![];

       // generated each string by adding small tweaks to the expected consensus "AATGCCCGTT"
       // convert sequences to Vec<u8>
       for seq in ["ATTGCCCGTT\0",
           "AATGCCGTT\0",
           "AATGCCCGAT\0",
           "AACGCCCGTC\0",
           "AGTGCTCGTT\0",
           "AATGCTCGTT\0"].iter() {
           seqs.push((*seq).bytes().map(|x|{x as u8}).collect::<Vec<u8>>());
       }

       // generate consensus sequence
       let consensus = poa_consensus(&seqs, 20, 1, 5, -4, -3, -1);

       let expected = "AATGCCCGTT".to_string().into_bytes();
       assert_eq!(consensus, expected);
   }