twitcher 0.1.9

Find template switch mutations in genomic data
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
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226

use std::{fmt::Debug, io::Write, sync::Arc};

use compact_genome::{
    implementation::{alphabets::dna_alphabet_or_n::DnaAlphabetOrN, vec_sequence::VectorGenome},
    interface::sequence::{GenomeSequence, OwnedGenomeSequence},
};
use csv::Writer;
use generic_a_star::cost::AStarCost;
use lib_tsalign::{
    a_star_aligner::{
        alignment_result::alignment::Alignment, template_switch_distance::AlignmentType,
    },
    config::TemplateSwitchConfig,
    costs::U64Cost,
};
use serde::{Deserialize, Serialize};

use crate::common::{
    ImmutableSequence, SequencePair,
    aligner::result::{TSData, TwitcherAlignmentWithStatistics},
    alignment::{ForwardAlignment, consumed_query},
    coords::GenomeRegion,
};

#[derive(Serialize, Deserialize)]
pub struct CSVRecord {
    pub cluster_id: String, // Some sort of running id (maybe even unique across files?), to make it easy to connect vcf and bam output.
    pub ref_ctx_region: String, // from aux data: entire region
    pub alt_ctx_region: String, // from aux data: entire region
    pub cluster_region: String, // from aux data: the region of the cluster, i.e. the "focus" region, will be a subregion of `region`
    pub ref_cluster_offset: usize,
    // pub ref_cluster_limit: usize,
    pub alt_cluster_offset: usize,
    // pub alt_cluster_limit: usize,
    pub ts_1_4_region: String, // TODO add 1-4 region for the template switches, might be useful for dedup
    pub read_id: Option<String>, // null if vcf
    pub fw_cigar: String,      // for cluster region
    pub fw_cigar_ctx: String,  // for context region
    pub fw_mi_ctx: String,     // for context region
    pub fw_cost: u64,          // for cluster region
    pub fw_cost_ctx: u64,      // for context region
    pub ts_cigar: String,      // for cluster region
    pub ts_cigar_ctx: String,  // for context region
    pub ts_cost: u64,          // for cluster region
    pub ts_cost_ctx: u64,      // for context region
    pub ts_num: usize,
    pub ts_1_2: String,
    pub ts_2_3: String,
    pub ts_1_4: String,
    pub ts_start_left_shift: String,
    pub ts_start_right_shift: String,
    pub ts_end_left_shift: String,
    pub ts_end_right_shift: String,
    pub ts_inner_alignment_cigar: String,
    // TODO some measure of repetition in the inner TS part? could be useful
}

static SEP: &str = "|";

pub struct TwitcherCSVWriter(Writer<Box<dyn Write + Send>>);

pub struct CSVAuxData {
    pub cluster_id: String,
    pub sequences: SequencePair,
    pub ref_context_region: GenomeRegion,
    pub alt_context_region: GenomeRegion,
    pub cluster_region: GenomeRegion,
    // pub ranges: AlignmentRange,
    pub alt_id: Option<String>,
    pub forward_alignment: ForwardAlignment,
    pub cost: Arc<TemplateSwitchConfig<DnaAlphabetOrN, U64Cost>>,
}

impl Debug for CSVAuxData {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        f.debug_struct("CSVAuxData")
            .field("cluster_id", &self.cluster_id)
            .field("sequences", &self.sequences)
            .field("ref_context_region", &self.ref_context_region)
            .field("alt_context_region", &self.alt_context_region)
            .field("cluster_region", &self.cluster_region)
            // .field("ref range", &self.re)
            // .field("alt range", &self.ranges.query_range())
            .field("alt_id", &self.alt_id)
            .field("forward_alignment", &self.forward_alignment.cigar())
            .field("cost", &"<cost def>")
            .finish()
    }
}

impl TwitcherCSVWriter {
    pub fn new(write: Box<dyn Write + Send>) -> Self {
        Self(Writer::from_writer(write))
    }

    pub fn write(
        &mut self,
        result: &TwitcherAlignmentWithStatistics,
        aux: CSVAuxData,
    ) -> anyhow::Result<()> {
        // dbg!(aux.forward_alignment.cigar());
        // dbg!(result.alignment.alignment.cigar());
        // dbg!(aux.sequences.reference.len());
        // dbg!(aux.sequences.query.len());

        let entire_forward_alignment = &aux.forward_alignment;
        let entire_forward_alignment_cost = compute_cost(
            &aux.sequences,
            None,
            entire_forward_alignment.0.clone(),
            &aux.cost,
        )?;
        let entire_ts_alignment = aux.forward_alignment.insert_ts_alignment(result)?;
        let entire_ts_alignment_cost =
            compute_cost(&aux.sequences, None, entire_ts_alignment.clone(), &aux.cost)?;
        let cluster_forward_alignment = aux.forward_alignment.crop_to_ts_region(result)?;
        let cluster_forward_alignment_cost = compute_cost(
            &aux.sequences,
            Some((result.stats.reference_offset(), result.stats.query_offset())),
            cluster_forward_alignment.clone(),
            &aux.cost,
        )?;
        let cluster_ts_alignment = &result.alignment.alignment;
        let cluster_ts_alignment_cost = result.alignment.cost.as_primitive();

        let ts_datas = TSData::compute(&aux.cluster_region, result)?;
        let ts_1_4_region = TSData::to_field(&ts_datas, SEP, |d| {
            if d.pos_1 <= d.pos_4 {
                GenomeRegion::from_incl_incl(d.pos_1.clone(), Some(d.pos_4.clone())).unwrap()
            } else {
                GenomeRegion::from_incl_incl(d.pos_4.clone(), Some(d.pos_1.clone())).unwrap()
            }
        });
        let record = CSVRecord {
            cluster_id: aux.cluster_id,
            ref_ctx_region: aux.ref_context_region.to_string(),
            alt_ctx_region: aux.alt_context_region.to_string(),
            cluster_region: aux.cluster_region.to_string(),
            ts_1_4_region,
            read_id: aux.alt_id,
            fw_cigar: cluster_forward_alignment.cigar(),
            fw_cigar_ctx: entire_forward_alignment.cigar(),
            fw_mi_ctx: create_mi_string(entire_forward_alignment, &aux.sequences.query),
            fw_cost: cluster_forward_alignment_cost,
            fw_cost_ctx: entire_forward_alignment_cost,
            ts_cigar: cluster_ts_alignment.cigar(),
            ts_cigar_ctx: entire_ts_alignment.cigar(),
            ts_cost: cluster_ts_alignment_cost,
            ts_cost_ctx: entire_ts_alignment_cost,
            ts_num: ts_datas.len(),
            ts_1_2: TSData::to_field(&ts_datas, SEP, |d| d.jump_1_2),
            ts_2_3: TSData::to_field(&ts_datas, SEP, |d| d.inner_len),
            ts_1_4: TSData::to_field(&ts_datas, SEP, |d| d.apg),
            ts_start_left_shift: TSData::to_field(&ts_datas, SEP, |d| -d.er.min_start),
            ts_start_right_shift: TSData::to_field(&ts_datas, SEP, |d| d.er.max_start),
            ts_end_left_shift: TSData::to_field(&ts_datas, SEP, |d| -d.er.min_end),
            ts_end_right_shift: TSData::to_field(&ts_datas, SEP, |d| d.er.max_end),
            ts_inner_alignment_cigar: TSData::to_field(&ts_datas, SEP, |d| d.inner_aln.cigar()),
            ref_cluster_offset: result.stats.reference_offset(),
            // ref_cluster_limit: aux.ranges.reference_limit(),
            alt_cluster_offset: result.stats.query_offset(),
            // alt_cluster_limit: aux.ranges.query_limit(),
        };

        // Write to csv
        tokio::task::block_in_place(|| self.0.serialize(record))?;

        Ok(())
    }

    pub fn flush(&mut self) -> std::io::Result<()> {
        self.0.flush()
    }
}

fn compute_cost(
    sequences: &SequencePair,
    sequence_offsets: Option<(usize, usize)>,
    mut alignment: Alignment<AlignmentType>,
    costs: &TemplateSwitchConfig<DnaAlphabetOrN, U64Cost>,
) -> anyhow::Result<u64> {
    let (r_off, q_off) = sequence_offsets.unwrap_or_default();
    // TODO this is copying data, which is a bit stupid but at the moment unavoidable due to the interfaces in lib_tsalign
    let r = VectorGenome::<DnaAlphabetOrN>::from_slice_u8(&sequences.reference[r_off..])?;
    let q = VectorGenome::from_slice_u8(&sequences.query[q_off..])?;
    // dbg!((r_off, q_off));
    // dbg!(sequences.reference[r_off..].len());
    // dbg!(sequences.reference[..].len());
    // dbg!(sequences.reference.as_bstr());
    // dbg!(sequences.query[q_off..].len());
    // dbg!(sequences.query[..].len());
    // dbg!(sequences.query.as_bstr());
    // dbg!(alignment.cigar());
    let cost = alignment.compute_cost(
        r.as_genome_subsequence(),
        q.as_genome_subsequence(),
        0,
        0,
        costs,
    );
    Ok(cost.as_primitive())
}

fn create_mi_string(forward_alignment: &ForwardAlignment, query: &ImmutableSequence) -> String {
    let mut qi = 0;
    let mut result = String::new();
    let mut counter = 0;
    for ty in forward_alignment.iter_flat() {
        match ty {
            AlignmentType::PrimaryInsertion | AlignmentType::PrimarySubstitution => {
                if counter > 0 {
                    result.push_str(&counter.to_string());
                    counter = 0;
                }
                result.push(char::from_u32(query[qi].into()).unwrap());
            }
            AlignmentType::PrimaryMatch => {
                counter += 1;
            }
            _ => {}
        }
        qi = (qi as isize + consumed_query(1, ty, None).unwrap()) as usize;
    }

    result
}