gskits 0.4.1

common kits
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

use std::{collections::HashMap, io::{self, BufRead}};

#[derive(Debug)]
pub struct VcfRowData {
    pub chrom: String,
    pub pos: usize, // zero based. 1-based in vcf file
    pub ref_bases: String,
    pub alt_bases: String,
    pub phred_q: u32,
}

impl VcfRowData {

    /// chrom pos id ref alt qual filter info format ..
    pub fn from_str(inp: &str) -> Self {
        let items = inp.split("\t").collect::<Vec<_>>();

        let chrom = items[0].trim().to_string();
        let pos = items[1].parse::<usize>().unwrap() - 1;
        let ref_bases = items[3].trim().to_string();
        let alt_bases = items[4].trim().to_string();
        let phred_q = items[5].parse::<u32>().unwrap();

        VcfRowData {
            chrom,
            pos, 
            ref_bases, 
            alt_bases, 
            phred_q
        }
    }

    #[allow(unused)]
    pub fn new(chrom: String, pos: usize, ref_bases: String, alt_bases: String, phred_q: u32) -> Self {
        Self { 
            chrom, 
            pos, 
            ref_bases, 
            alt_bases, 
            phred_q
        }
    }

}

pub struct VcfReaderIter<'a> {
    reader: &'a mut dyn io::BufRead
}

impl <'a> VcfReaderIter<'a>{
    
    pub fn new(reader: &'a mut dyn io::BufRead) -> Self {
        VcfReaderIter { reader: reader }
    }

}

impl<'a> Iterator for VcfReaderIter<'a> {
    type Item = VcfRowData;

    fn next(&mut self) -> Option<Self::Item> {
        
        let mut line = String::new();
        loop {
            line.clear();
            if let Ok(n) = self.reader.read_line(&mut line) {
                if n == 0 {
                    return None;
                }
                if line.starts_with("#") {
                    continue;
                }

                return Some(VcfRowData::from_str(&line));
            } else {
                return None;
            }

        }

    }

}


pub struct VcfInfo {
    info: HashMap<String, Vec<usize>>,
}

impl VcfInfo {
    pub fn new(file_reader: &mut dyn BufRead) -> Self {
        let mut info = HashMap::new();
        let file_iter = VcfReaderIter::new(file_reader);
        file_iter.for_each(|vcf| {
            // .into_iter().collect::<Vec<usize>>()
            let bad_points = vcf.pos..(vcf.pos + vcf.ref_bases.len()) ;
            info.entry(vcf.chrom).or_insert(vec![]).extend(bad_points);

        });

        info.iter_mut().for_each(|(_k, v)| {
            v.sort_unstable();
        });

        Self { 
            info
        }
    }

    /// true: means the range contains a variant loci
    pub fn range_hit(&self, chromosome: &str, range: &(usize, usize)) -> bool {
        
        if !self.info.contains_key(chromosome) {
            return false;
        }

        let sorted_vec = self.info.get(chromosome).unwrap();
        return match sorted_vec.binary_search(&range.0) {
            Ok(_) => true,
            Err(n) => {
                if n == sorted_vec.len() {
                    false
                } else {
                    if range.1 <= sorted_vec[n] {
                        false
                    } else {
                        true
                    }
                }
            }
        };
    }

}