lib_tsalign 1.0.1

A sequence-to-sequence aligner that accounts for template switches
Documentation 
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use compact_genome::implementation::alphabets::dna_alphabet::DnaAlphabet;
use generic_a_star::cost::U64Cost;

use crate::costs::gap_affine::GapAffineAlignmentCostTable;

#[test]
fn simple_example() {
    let input = "# Simple Example\n\nSubstitutionCostTable\n  |  A  C  G  T\n--+------------\nA | 10  9 11  7\nC |  2  1  3  4\nG |  5  6 17  8\nT | 99  0 50 51\n\nGapOpenCostVector\n A C G T\n 3 4 5 1\n\nGapExtendCostVector\n  A  C  G  T\n 10 15  0  1\n";
    let expected_parsing_result = GapAffineAlignmentCostTable::<DnaAlphabet, U64Cost>::new(
        "Simple Example".to_string(),
        [10u64, 9, 11, 7, 2, 1, 3, 4, 5, 6, 17, 8, 99, 0, 50, 51]
            .into_iter()
            .map(Into::into)
            .collect::<Vec<_>>(),
        [3u64, 4, 5, 1]
            .into_iter()
            .map(Into::into)
            .collect::<Vec<_>>(),
        [10u64, 15, 0, 1]
            .into_iter()
            .map(Into::into)
            .collect::<Vec<_>>(),
    );

    let actual_parsing_result =
        GapAffineAlignmentCostTable::<DnaAlphabet, U64Cost>::read_plain(input.as_bytes()).unwrap();
    let mut writer = Vec::new();
    actual_parsing_result.write_plain(&mut writer).unwrap();
    let output = String::from_utf8(writer).unwrap();

    assert_eq!(expected_parsing_result, actual_parsing_result);
    assert_eq!(input, output);
}