lib_ts_chainalign 4.0.1

A chaining-based sequence-to-sequence aligner that accounts for template switches
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
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

use generic_a_star::{AStar, AStarBuffers, AStarResult, cost::AStarCost};

use crate::{
    alignment::{Alignment, coordinates::AlignmentCoordinates, sequences::AlignmentSequences},
    anchors::{primary::PrimaryAnchor, secondary::SecondaryAnchor},
    costs::GapAffineCosts,
    exact_chaining::gap_affine::algo::{Context, Node},
};

mod algo;
#[cfg(test)]
mod tests;

pub struct GapAffineAligner<'sequences, 'cost_table, 'rc_fn, Cost: AStarCost> {
    a_star_buffers: Option<AStarBuffers<Node<Cost>>>,
    sequences: &'sequences AlignmentSequences,
    cost_table: &'cost_table GapAffineCosts<Cost>,
    rc_fn: &'rc_fn dyn Fn(u8) -> u8,
    max_match_run: u32,
}

impl<'sequences, 'cost_table, 'rc_fn, Cost: AStarCost>
    GapAffineAligner<'sequences, 'cost_table, 'rc_fn, Cost>
{
    pub fn new(
        sequences: &'sequences AlignmentSequences,
        cost_table: &'cost_table GapAffineCosts<Cost>,
        rc_fn: &'rc_fn dyn Fn(u8) -> u8,
        max_match_run: u32,
    ) -> Self {
        Self {
            a_star_buffers: Some(Default::default()),
            sequences,
            cost_table,
            rc_fn,
            max_match_run,
        }
    }

    fn allow_direct_chaining(
        &self,
        start: AlignmentCoordinates,
        end: AlignmentCoordinates,
    ) -> bool {
        start == self.sequences.primary_start() || end == self.sequences.primary_end()
    }

    fn allow_all_matches(&self, start: AlignmentCoordinates, end: AlignmentCoordinates) -> bool {
        let minimum_primary_sequence_length =
            (self.sequences.primary_end().primary_ordinate_a().unwrap()
                - self.sequences.primary_start().primary_ordinate_a().unwrap())
            .min(
                self.sequences.primary_end().primary_ordinate_b().unwrap()
                    - self.sequences.primary_start().primary_ordinate_b().unwrap(),
            );
        start == self.sequences.primary_start()
            && end == self.sequences.primary_end()
            && u32::try_from(minimum_primary_sequence_length).unwrap() <= self.max_match_run
    }

    /// Align from start to end.
    ///
    /// Additionally continue the alignment to all nodes with the same cost as the alignment cost from start to end.
    ///
    /// Collect all closed nodes into the given output lists.
    /// Note that the output lists may contain duplicate anchors with different cost.
    pub fn align(
        &mut self,
        start: AlignmentCoordinates,
        end: AlignmentCoordinates,
        additional_primary_targets_output: &mut impl Extend<(PrimaryAnchor, Cost)>,
        additional_secondary_targets_output: &mut impl Extend<(SecondaryAnchor, Cost)>,
    ) -> (Cost, Alignment) {
        assert!(
            start.is_primary() && end.is_primary() || start.is_secondary() && end.is_secondary()
        );

        let context = Context::new(
            self.cost_table,
            self.sequences,
            self.rc_fn,
            start,
            end,
            self.allow_direct_chaining(start, end),
            self.allow_all_matches(start, end),
            self.max_match_run,
        );
        let mut a_star = AStar::new_with_buffers(context, self.a_star_buffers.take().unwrap());

        a_star.initialise();
        let (cost, alignment) = match a_star.search() {
            AStarResult::FoundTarget { cost, .. } => {
                let alignment = a_star.reconstruct_path().into();
                (cost.0, alignment)
            }
            AStarResult::ExceededCostLimit { .. } => unreachable!("Cost limit is None"),
            AStarResult::ExceededMemoryLimit { .. } => unreachable!("Cost limit is None"),
            AStarResult::NoTarget => (Cost::max_value(), Vec::new().into()),
        };
        a_star.search_until_with_target_policy(|_, node| node.cost > cost, true);

        self.fill_additional_targets(
            &a_star,
            start,
            additional_primary_targets_output,
            additional_secondary_targets_output,
        );
        self.a_star_buffers = Some(a_star.into_buffers());

        (cost, alignment)
    }

    /// Align from start until the cost limit is reached.
    ///
    /// Collect all closed nodes into the given output lists.
    /// Note that the output lists may contain duplicate anchors with different cost.
    pub fn align_until_cost_limit(
        &mut self,
        start: AlignmentCoordinates,
        cost_limit: Cost,
        additional_primary_targets_output: &mut impl Extend<(PrimaryAnchor, Cost)>,
        additional_secondary_targets_output: &mut impl Extend<(SecondaryAnchor, Cost)>,
    ) {
        let end = self.sequences.end(start.ts_kind());
        debug_assert!(
            start.is_primary() && end.is_primary() || start.is_secondary() && end.is_secondary()
        );

        let context = Context::new(
            self.cost_table,
            self.sequences,
            self.rc_fn,
            start,
            end,
            true,
            true,
            self.max_match_run,
        );
        let mut a_star = AStar::new_with_buffers(context, self.a_star_buffers.take().unwrap());
        a_star.initialise();
        a_star.search_until_with_target_policy(|_, node| node.cost > cost_limit, true);

        self.fill_additional_targets(
            &a_star,
            start,
            additional_primary_targets_output,
            additional_secondary_targets_output,
        );
        self.a_star_buffers = Some(a_star.into_buffers());
    }

    fn fill_additional_targets(
        &self,
        a_star: &AStar<Context<Cost>>,
        start: AlignmentCoordinates,
        additional_primary_targets_output: &mut impl Extend<(PrimaryAnchor, Cost)>,
        additional_secondary_targets_output: &mut impl Extend<(SecondaryAnchor, Cost)>,
    ) {
        additional_primary_targets_output.extend(
            a_star
                .iter_closed_nodes()
                .filter(|node| node.identifier.coordinates.is_primary())
                .filter(|node| {
                    start != node.identifier.coordinates
                        || self.allow_direct_chaining(start, node.identifier.coordinates)
                })
                .filter(|node| {
                    start == node.identifier.coordinates
                        || node.identifier.has_non_match
                        || self.allow_all_matches(start, node.identifier.coordinates)
                })
                .filter(|node| {
                    // Filter duplicates.
                    let mut pair_identifier = node.identifier;
                    pair_identifier.has_non_match = !pair_identifier.has_non_match;
                    a_star
                        .closed_node(&pair_identifier)
                        .map(|pair| {
                            pair.cost > node.cost
                                || (pair.cost == node.cost && node.identifier.has_non_match)
                        })
                        .unwrap_or(true)
                })
                .map(|node| {
                    (
                        PrimaryAnchor::new_from_start(&node.identifier.coordinates),
                        node.cost,
                    )
                }),
        );
        additional_secondary_targets_output.extend(
            a_star
                .iter_closed_nodes()
                .filter(|node| node.identifier.coordinates.is_secondary())
                .filter(|node| {
                    start != node.identifier.coordinates
                        || self.allow_direct_chaining(start, node.identifier.coordinates)
                })
                .filter(|node| {
                    start == node.identifier.coordinates
                        || node.identifier.has_non_match
                        || self.allow_all_matches(start, node.identifier.coordinates)
                })
                .filter(|node| {
                    // Filter duplicates.
                    let mut pair_identifier = node.identifier;
                    pair_identifier.has_non_match = !pair_identifier.has_non_match;
                    a_star
                        .closed_node(&pair_identifier)
                        .map(|pair| {
                            pair.cost > node.cost
                                || (pair.cost == node.cost && node.identifier.has_non_match)
                        })
                        .unwrap_or(true)
                })
                .map(|node| {
                    (
                        SecondaryAnchor::new_from_start(&node.identifier.coordinates),
                        node.cost,
                    )
                }),
        );
    }
}