mm2 0.26.0

minimap2 frontend
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173

use crate::mapping_ext::MappingExt;

const GAP: u8 = '-' as u8;

fn shift(aligned_target: &mut [u8], aligned_seq: &mut [u8], cur_idx: usize) {
    for idx in cur_idx..(aligned_target.len() - 1) {
        let target_cur_base = aligned_target[idx];
        if target_cur_base != GAP
            && aligned_target[idx + 1] == GAP
            && target_cur_base == aligned_seq[idx]
            && target_cur_base == aligned_seq[idx + 1]
        {
            aligned_target.swap(idx, idx + 1);
        } else {
            break;
        }
    }
}

fn compute_cigar_state(target_aligned_base: u8, query_aligned_base: u8) -> u8 {
    if target_aligned_base == GAP {
        return 1; // ins
    }
    if query_aligned_base == GAP {
        return 2; // del
    }

    if query_aligned_base == target_aligned_base {
        return 7; // eq
    }

    if query_aligned_base != target_aligned_base {
        return 8; // mismatch
    }

    return 0;
}

/// Vec<(u32, u8)>
fn aligned_pair_seqs_2_cigar(aligned_target: &[u8], aligned_seq: &[u8]) -> Vec<(u32, u8)> {
    let mut cigars = vec![];
    let mut cur_state = (
        1_u32,
        compute_cigar_state(aligned_target[0], aligned_seq[0]),
    );

    for idx in 1..aligned_target.len() {
        let cigar_state = compute_cigar_state(aligned_target[idx], aligned_seq[idx]);
        if cigar_state == cur_state.1 {
            cur_state.0 += 1;
        } else {
            cigars.push(cur_state);
            cur_state = (1, cigar_state);
        }
    }
    cigars.push(cur_state);
    cigars
}

pub fn cigar_adjust_poly_gap_left_align(
    hit: &mut minimap2::Mapping,
    target_seq: &[u8],
    query_seq: &[u8],
) {
    // hit.alignment.unwrap().cigar
    let hit_ext = MappingExt(hit);

    let (mut aligned_target, mut aligned_seq) = hit_ext.aligned_2_str(target_seq, query_seq);

    let aligned_target = unsafe { aligned_target.as_bytes_mut() };
    let aligned_seq = unsafe { aligned_seq.as_bytes_mut() };

    for cur_idx in (0..(aligned_target.len() - 1)).rev() {
        shift(aligned_target, aligned_seq, cur_idx);
    }

    println!("{:?}", hit.alignment.as_ref().unwrap().cigar);
    let new_cigars = aligned_pair_seqs_2_cigar(aligned_target, aligned_seq);
    hit.alignment.as_mut().unwrap().cigar = Some(new_cigars);
}

#[cfg(test)]
mod test {
    use minimap2::Aligner;

    use crate::{
        cigar_adjust::cigar_adjust_poly_gap_left_align, mapping_ext::MappingExt, visualization,
    };

    #[test]
    fn test_cigar_adjust_poly_gap_left_align_1() {
        let target_seq = "GGGGGGGGGGGGGGGGGCCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATTCCCCCGGTCCACCTGGTCTCTCCACCTTAGGTACAAAGACGGTTCGGCACTGCCGTAGAATTTCGGGTATTTCGCCTCGTGCCATCCATGCATTGAACATTTCCGCCTTCAAGTGCACAGGAACCGCACGCCACTGACCCGAACGTATACCGTCCGGGCCCGGCGAAGTTCGCCAGTCAAAGCGGGAGGCCTTGATCTCTTCCACCGAGATCGGCTTCCACAGCTGGGTGTAGTCGCGATTAGACCCAATTCCTGCTATCCCCAAGCACCGCGTCCAGTACTGCGGAATTCTCCAGCGTACCGTCGGCGCAGATAAATCCGCGCTGTCGTGCATCAGGGGGGCAGCAAGCCAACAGCCTCCGGG";
        let query_seq = "CCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATTCCCCCCGGGTCCACCTGGTCTCTCCACCTTAGGTACAAAGACGGTCGGCACTGCCGTAGAATTTCGGGTATTTCGCCTCGTGCCATCCATGCATTGAACATTTCCGCCTTCAAGTGCACAGGAACCGCACGCCACTGACCCGAACGTATACCGTCCGGGCCCGGCGAAGTTCGCCAGTCAAAGCGGGAGGCCTTGATCTCTTCCACCGAGATCGGCTTCCACAGCTGGGTGTAGTCGCGATTAGACCCAATTCCTGCTATCCCCAAGCACCGCGTCCAGTACTGCGGAATTCTCCAGCGTACCGTCGGGCGCAGATAAATCCGCGCTGTCGTGCATCAGGGGGGCAGCAAGCCAACAGCCTCGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";

        let aligner = Aligner::builder()
            .map_ont()
            .with_cigar()
            .with_sam_out()
            .with_sam_hit_only();

        let aligner = aligner
            .with_seq_and_id(target_seq.as_bytes(), b"ref")
            .unwrap();

        for mut hit in aligner
            .map(
                query_seq.as_bytes(),
                false,
                false,
                None,
                Some(&[67108864, 68719476736]),
                Some(b"q"),
            )
            .unwrap()
        {
            visualization::blast_like_alignment(query_seq, target_seq, &hit, None);

            cigar_adjust_poly_gap_left_align(&mut hit, target_seq.as_bytes(), query_seq.as_bytes());

            let hit_ext = MappingExt(&hit);

            let (aligned_target, aligned_seq) =
                hit_ext.aligned_2_str(target_seq.as_bytes(), query_seq.as_bytes());

            assert_eq!(&aligned_target[..100], "CCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATT-CCCCC-GGTCCACCTGGTCTCTCCACCTTAGGTACAAAGACG");
            assert_eq!(&aligned_seq[..100],    "CCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATTCCCCCCGGGTCCACCTGGTCTCTCCACCTTAGGTACAAAGACG");

            visualization::blast_like_alignment(query_seq, target_seq, &hit, None);
        }
    }

    #[test]
    fn test_cigar_adjust_poly_gap_left_align_2() {
        let target_seq = "GGGGGGGGGGGGGGGGGCCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATTCCCCCGGTCCACCTGGTCTCTCCACCTTAGGTACAAAGACGGTTCGGCACTGCCGTAGAATTTCGGGTATTTCGCCTCGTGCCATCCATGCATTGAACATTTCCGCCTTCAAGTGCACAGGAACCGCACGCCACTGACCCGAACGTATACCGTCCGGGCCCGGCGAAGTTCGCCAGTCAAAGCGGGAGGCCTTGATCTCTTCCACCGAGATCGGCTTCCACAGCTGGGTGTAGTCGCGATTAGACCCAATTCCTGCTATCCCCAAGCACCGCGTCCAGTACTGCGGAATTCTCCAGCGTACCGTCGGCGCAGATAAATCCGCGCTGTCGTGCATCAGGGGGGCAGCAAGCCAACAGCCTCCGGG";
        let query_seq = "CCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATTCCCCCCCCGGGGTCCACCTGGTCTCTCCACCTTAGGTACAAAGACGGTCGGCACTGCCGTAGAATTTCGGGTATTTCGCCTCGTGCCATCCATGCATTGAACATTTCCGCCTTCAAGTGCACAGGAACCGCACGCCACTGACCCGAACGTATACCGTCCGGGCCCGGCGAAGTTCGCCAGTCAAAGCGGGAGGCCTTGATCTCTTCCACCGAGATCGGCTTCCACAGCTGGGTGTAGTCGCGATTAGACCCAATTCCTGCTATCCCCAAGCACCGCGTCCAGTACTGCGGAATTCTCCAGCGTACCGTCGGGCGCAGATAAATCCGCGCTGTCGTGCATCAGGGGGGCAGCAAGCCAACAGCCTCGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";

        let aligner = Aligner::builder()
            .map_ont()
            .with_cigar()
            .with_sam_out()
            .with_sam_hit_only();

        let aligner = aligner
            .with_seq_and_id(target_seq.as_bytes(), b"ref")
            .unwrap();

        for mut hit in aligner
            .map(
                query_seq.as_bytes(),
                false,
                false,
                None,
                Some(&[67108864, 68719476736]),
                Some(b"q"),
            )
            .unwrap()
        {
            visualization::blast_like_alignment(query_seq, target_seq, &hit, None);

            cigar_adjust_poly_gap_left_align(&mut hit, target_seq.as_bytes(), query_seq.as_bytes());

            let hit_ext = MappingExt(&hit);

            let (aligned_target, aligned_seq) =
                hit_ext.aligned_2_str(target_seq.as_bytes(), query_seq.as_bytes());

            assert_eq!(&aligned_target[..100], "CCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATT---CCCCC--GGTCCACCTGGTCTCTCCACCTTAGGTACAAAG");
            assert_eq!(&aligned_seq[..100],    "CCAAGATGGAGTGAAAGTGTCTCAGGGGAATCGACGCGATCGAGATCGGTCGATATTCCCCCCCCGGGGTCCACCTGGTCTCTCCACCTTAGGTACAAAG");

            visualization::blast_like_alignment(query_seq, target_seq, &hit, None);
        }
    }
}