chaintools 0.0.2

work with .chain files in Rust
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

use chaintools::storage::{ByteSlice, SharedBytes};
use chaintools::{Chain, Strand};

#[test]
fn strand_creation() {
    let plus = Strand::Plus;
    let minus = Strand::Minus;

    assert_eq!(plus, Strand::Plus);
    assert_eq!(minus, Strand::Minus);
    assert_ne!(plus, minus);
}

#[test]
fn strand_copy_and_clone() {
    let original = Strand::Plus;
    let copied = original;
    let cloned = original.clone();

    assert_eq!(original, copied);
    assert_eq!(original, cloned);
}

#[test]
fn chain_creation() {
    let storage = SharedBytes::from_owned(b"chrYchr5".to_vec());
    let reference_name = ByteSlice::new(storage.clone(), 0..4);
    let query_name = ByteSlice::new(storage.clone(), 4..8);

    let chain = Chain {
        score: 4900,
        reference_name,
        reference_size: 58368225,
        reference_strand: Strand::Plus,
        reference_start: 25985403,
        reference_end: 25985638,
        query_name,
        query_size: 151006098,
        query_strand: Strand::Minus,
        query_start: 43257292,
        query_end: 43257528,
        id: 1,
        blocks: chaintools::BlockSlice::new(
            std::sync::Arc::new(vec![
                chaintools::Block {
                    size: 9,
                    gap_reference: 1,
                    gap_query: 0,
                },
                chaintools::Block {
                    size: 10,
                    gap_reference: 0,
                    gap_query: 5,
                },
            ]),
            0..2,
        ),
    };

    assert_eq!(chain.score, 4900);
    assert_eq!(chain.reference_name.as_str(), Some("chrY"));
    assert_eq!(chain.query_name.as_str(), Some("chr5"));
    assert_eq!(chain.reference_strand, Strand::Plus);
    assert_eq!(chain.query_strand, Strand::Minus);
    assert_eq!(chain.id, 1);
    assert_eq!(chain.blocks.as_slice().len(), 2);
}

#[test]
fn chain_clone() {
    let storage = SharedBytes::from_owned(b"chrYchr5".to_vec());
    let reference_name = ByteSlice::new(storage.clone(), 0..4);
    let query_name = ByteSlice::new(storage.clone(), 4..7);

    let chain = Chain {
        score: 100,
        reference_name,
        reference_size: 1000,
        reference_strand: Strand::Plus,
        reference_start: 0,
        reference_end: 100,
        query_name,
        query_size: 1000,
        query_strand: Strand::Plus,
        query_start: 0,
        query_end: 100,
        id: 1,
        blocks: chaintools::BlockSlice::new(
            std::sync::Arc::new(vec![chaintools::Block {
                size: 100,
                gap_reference: 0,
                gap_query: 0,
            }]),
            0..1,
        ),
    };

    let cloned = chain.clone();
    assert_eq!(chain.score, cloned.score);
    assert_eq!(chain.id, cloned.id);
    assert_eq!(
        chain.reference_name.as_str(),
        cloned.reference_name.as_str()
    );
    assert_eq!(chain.query_name.as_str(), cloned.query_name.as_str());
}

#[test]
fn chain_debug_format() {
    let storage = SharedBytes::from_owned(b"chrYchr5".to_vec());
    let reference_name = ByteSlice::new(storage.clone(), 0..4);
    let query_name = ByteSlice::new(storage.clone(), 4..7);

    let chain = Chain {
        score: 100,
        reference_name,
        reference_size: 1000,
        reference_strand: Strand::Plus,
        reference_start: 0,
        reference_end: 100,
        query_name,
        query_size: 1000,
        query_strand: Strand::Plus,
        query_start: 0,
        query_end: 100,
        id: 1,
        blocks: chaintools::BlockSlice::new(
            std::sync::Arc::new(vec![chaintools::Block {
                size: 100,
                gap_reference: 0,
                gap_query: 0,
            }]),
            0..1,
        ),
    };

    let debug_str = format!("{:?}", chain);
    assert!(debug_str.contains("Chain"));
    assert!(debug_str.contains("score: 100"));
    assert!(debug_str.contains("id: 1"));
}