chaintools 0.0.3

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
142
143
144
145
146
147

// Integration tests for parsing functionality
// Tests the public API that uses the private parser modules

use chaintools::{Reader, StreamingReader};

const COMPLEX_CHAIN: &str = "chain 1000 chr1 10000 + 1000 2000 chr2 8000 - 500 1500 42\n\
100 10 5\n\
200 0 20\n\
50 15 0\n\
300 5 10\n\
150 0 0\n\
\n";

const MALFORMED_CHAINS: &str = "invalid line\n\
chain 100 chr1 1000 + 0 100 chr2 1000 + 0 100 1\n\
50\n\
\n\
chain missing fields\n\
\n";

#[test]
fn parse_complex_chain() {
    let reader = Reader::from_owned_bytes(COMPLEX_CHAIN.as_bytes().to_vec()).unwrap();
    assert_eq!(reader.len(), 1);

    let chain = reader.chains().next().unwrap();
    assert_eq!(chain.score, 1000);
    assert_eq!(chain.id, 42);
    assert_eq!(chain.reference_name.as_str(), Some("chr1"));
    assert_eq!(chain.query_name.as_str(), Some("chr2"));
    assert_eq!(chain.reference_strand, chaintools::Strand::Plus);
    assert_eq!(chain.query_strand, chaintools::Strand::Minus);

    // Check blocks
    let blocks = chain.blocks.as_slice();
    assert_eq!(blocks.len(), 5);

    assert_eq!(blocks[0].size, 100);
    assert_eq!(blocks[0].gap_reference, 10);
    assert_eq!(blocks[0].gap_query, 5);

    assert_eq!(blocks[1].size, 200);
    assert_eq!(blocks[1].gap_reference, 0);
    assert_eq!(blocks[1].gap_query, 20);

    assert_eq!(blocks[2].size, 50);
    assert_eq!(blocks[2].gap_reference, 15);
    assert_eq!(blocks[2].gap_query, 0);

    assert_eq!(blocks[3].size, 300);
    assert_eq!(blocks[3].gap_reference, 5);
    assert_eq!(blocks[3].gap_query, 10);

    assert_eq!(blocks[4].size, 150);
    assert_eq!(blocks[4].gap_reference, 0);
    assert_eq!(blocks[4].gap_query, 0);
}

#[test]
fn parse_malformed_chains() {
    let result = Reader::from_owned_bytes(MALFORMED_CHAINS.as_bytes().to_vec());
    assert!(result.is_err(), "Should fail on malformed input");
}

#[test]
fn streaming_parse_complex_chain() {
    use std::io::{BufReader, Cursor};

    let cursor = Cursor::new(COMPLEX_CHAIN.as_bytes());
    let mut reader = StreamingReader::new(BufReader::new(cursor));

    let chain = reader
        .next_chain()
        .unwrap()
        .expect("Should parse complex chain");
    assert_eq!(chain.score, 1000);
    assert_eq!(chain.blocks.len(), 5);

    let result = reader.next_chain().unwrap();
    assert!(result.is_none(), "Should return None after parsing");
}

#[test]
fn parse_chain_with_large_coordinates() {
    let data = "chain 9223372036854775807 chr1 4294967295 + 0 4294967295 chr2 4294967295 + 0 4294967295 18446744073709551615\n4294967295\n4294967295\n\n";

    let reader = Reader::from_owned_bytes(data.as_bytes().to_vec()).unwrap();
    let chain = reader.chains().next().unwrap();

    assert_eq!(chain.score, 9223372036854775807); // i64::MAX
    assert_eq!(chain.reference_size, 4294967295); // u32::MAX
    assert_eq!(chain.query_size, 4294967295); // u32::MAX
    assert_eq!(chain.id, 18446744073709551615); // u64::MAX
    assert_eq!(chain.blocks.as_slice()[0].size, 4294967295);
}

#[test]
fn parse_chain_with_minimal_blocks() {
    let data = "chain 1 chr1 100 + 0 100 chr2 100 + 0 100 1\n1\n\n";

    let reader = Reader::from_owned_bytes(data.as_bytes().to_vec()).unwrap();
    let chain = reader.chains().next().unwrap();

    assert_eq!(chain.score, 1);
    assert_eq!(chain.blocks.as_slice().len(), 1);
    assert_eq!(chain.blocks.as_slice()[0].size, 1);
    assert_eq!(chain.blocks.as_slice()[0].gap_reference, 0);
    assert_eq!(chain.blocks.as_slice()[0].gap_query, 0);
}

#[test]
fn parse_chain_with_zero_size_blocks() {
    let data = "chain 1 chr1 100 + 0 100 chr2 100 + 0 100 1\n0 10 5\n10 0 0\n\n";

    let reader = Reader::from_owned_bytes(data.as_bytes().to_vec()).unwrap();
    let chain = reader.chains().next().unwrap();

    assert_eq!(chain.blocks.as_slice().len(), 2);
    assert_eq!(chain.blocks.as_slice()[0].size, 0);
    assert_eq!(chain.blocks.as_slice()[0].gap_reference, 10);
    assert_eq!(chain.blocks.as_slice()[0].gap_query, 5);
}

#[test]
fn parse_multiple_chains_with_different_strands() {
    let data = "chain 100 chr1 1000 + 0 100 chr2 1000 + 0 100 1\n50\n50\n\n\
chain 200 chr1 1000 - 0 100 chr2 1000 - 0 100 2\n60\n60\n\n\
chain 300 chr1 1000 + 0 100 chr2 1000 - 0 100 3\n70\n70\n\n\
chain 400 chr1 1000 - 0 100 chr2 1000 + 0 100 4\n80\n80\n\n";

    let reader = Reader::from_owned_bytes(data.as_bytes().to_vec()).unwrap();
    assert_eq!(reader.len(), 4);

    let chains: Vec<_> = reader.chains().collect();

    assert_eq!(chains[0].reference_strand, chaintools::Strand::Plus);
    assert_eq!(chains[0].query_strand, chaintools::Strand::Plus);

    assert_eq!(chains[1].reference_strand, chaintools::Strand::Minus);
    assert_eq!(chains[1].query_strand, chaintools::Strand::Minus);

    assert_eq!(chains[2].reference_strand, chaintools::Strand::Plus);
    assert_eq!(chains[2].query_strand, chaintools::Strand::Minus);

    assert_eq!(chains[3].reference_strand, chaintools::Strand::Minus);
    assert_eq!(chains[3].query_strand, chaintools::Strand::Plus);
}