lib_ts_chainalign 2.1.2

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

use generic_a_star::cost::{AStarCost, U32Cost};

use crate::{
    chaining_lower_bounds::ts_jump::TsJumpLowerBounds,
    costs::{AlignmentCosts, GapAffineCosts, TsLimits},
};

#[test]
fn test_max_match_run_0() {
    let cost_table = AlignmentCosts {
        primary_costs: GapAffineCosts {
            substitution: U32Cost::from(2u8),
            gap_open: U32Cost::from(3u8),
            gap_extend: U32Cost::from(1u8),
        },
        secondary_costs: GapAffineCosts {
            substitution: U32Cost::from(4u8),
            gap_open: U32Cost::from(6u8),
            gap_extend: U32Cost::from(2u8),
        },
        ts_base_cost: U32Cost::from(2u8).into(),
        ts_limits: TsLimits {
            inter_jump_12: -100..100,
            intra_jump_12: -100..100,
            jump_34: -100..100,
            length_23: 0..200,
            ancestor_gap: -100..100,
        },
    };

    let max_n = 2;
    let lower_bounds = TsJumpLowerBounds::new(max_n, 0, &cost_table);

    let expected_lower_bounds_12 = [2, 4, 6];
    let expected_lower_bounds_34 =
        expected_lower_bounds_12.map(|cost| cost - cost_table.ts_base_cost.min().as_primitive());

    for descendant_gap in 0..=max_n {
        assert_eq!(
            lower_bounds.lower_bound_12(descendant_gap).as_primitive(),
            expected_lower_bounds_12[descendant_gap],
            "lower_bound_12({})",
            descendant_gap
        );
        assert_eq!(
            lower_bounds.lower_bound_34(descendant_gap).as_primitive(),
            expected_lower_bounds_34[descendant_gap],
            "lower_bound_34({})",
            descendant_gap
        );
    }
}

#[test]
fn test_max_match_run_1() {
    let cost_table = AlignmentCosts {
        primary_costs: GapAffineCosts {
            substitution: U32Cost::from(2u8),
            gap_open: U32Cost::from(3u8),
            gap_extend: U32Cost::from(1u8),
        },
        secondary_costs: GapAffineCosts {
            substitution: U32Cost::from(4u8),
            gap_open: U32Cost::from(6u8),
            gap_extend: U32Cost::from(2u8),
        },
        ts_base_cost: U32Cost::from(2u8).into(),
        ts_limits: TsLimits {
            inter_jump_12: -100..100,
            intra_jump_12: -100..100,
            jump_34: -100..100,
            length_23: 0..200,
            ancestor_gap: -100..100,
        },
    };

    let max_n = 8;
    let lower_bounds = TsJumpLowerBounds::new(max_n, 1, &cost_table);

    let expected_lower_bounds_12 = [2, 2, 2, 4, 4, 6, 6, 8, 8];
    let expected_lower_bounds_34 =
        expected_lower_bounds_12.map(|cost| cost - cost_table.ts_base_cost.min().as_primitive());

    for descendant_gap in 0..=max_n {
        assert_eq!(
            lower_bounds.lower_bound_12(descendant_gap).as_primitive(),
            expected_lower_bounds_12[descendant_gap],
            "lower_bound_12({})",
            descendant_gap
        );
        assert_eq!(
            lower_bounds.lower_bound_34(descendant_gap).as_primitive(),
            expected_lower_bounds_34[descendant_gap],
            "lower_bound_34({})",
            descendant_gap
        );
    }
}

#[test]
fn test_max_match_run_2() {
    let cost_table = AlignmentCosts {
        primary_costs: GapAffineCosts {
            substitution: U32Cost::from(2u8),
            gap_open: U32Cost::from(3u8),
            gap_extend: U32Cost::from(1u8),
        },
        secondary_costs: GapAffineCosts {
            substitution: U32Cost::from(4u8),
            gap_open: U32Cost::from(6u8),
            gap_extend: U32Cost::from(2u8),
        },
        ts_base_cost: U32Cost::from(2u8).into(),
        ts_limits: TsLimits {
            inter_jump_12: -100..100,
            intra_jump_12: -100..100,
            jump_34: -100..100,
            length_23: 0..200,
            ancestor_gap: -100..100,
        },
    };

    let max_n = 9;
    let lower_bounds = TsJumpLowerBounds::new(max_n, 2, &cost_table);

    let expected_lower_bounds_12 = [2, 2, 2, 2, 2, 4, 4, 4, 6, 6];
    let expected_lower_bounds_34 =
        expected_lower_bounds_12.map(|cost| cost - cost_table.ts_base_cost.min().as_primitive());

    for descendant_gap in 0..=max_n {
        assert_eq!(
            lower_bounds.lower_bound_12(descendant_gap).as_primitive(),
            expected_lower_bounds_12[descendant_gap],
            "lower_bound_12({})",
            descendant_gap
        );
        assert_eq!(
            lower_bounds.lower_bound_34(descendant_gap).as_primitive(),
            expected_lower_bounds_34[descendant_gap],
            "lower_bound_34({})",
            descendant_gap
        );
    }
}