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

use std::{
    io::{self, Read, Seek},
    vec,
};

use noodles_bgzf as bgzf;
use noodles_core::region::Interval;
use noodles_csi::index::reference_sequence::bin::Chunk;

use super::Reader;
use crate::{Header, Record};

enum State {
    Seek,
    Read(bgzf::VirtualPosition),
    Done,
}

/// An iterator over records of a VCF reader that intersects a given region.
///
/// This is created by calling [`Reader::query`].
pub struct Query<'r, 'h, R>
where
    R: Read + Seek + 'r,
{
    reader: &'r mut Reader<bgzf::Reader<R>>,

    chunks: vec::IntoIter<Chunk>,

    reference_sequence_name: String,
    interval: Interval,

    state: State,
    header: &'h Header,

    record: Record,
}

impl<'r, 'h, R> Query<'r, 'h, R>
where
    R: Read + Seek,
{
    pub(super) fn new(
        reader: &'r mut Reader<bgzf::Reader<R>>,
        chunks: Vec<Chunk>,
        reference_sequence_name: String,
        interval: Interval,
        header: &'h Header,
    ) -> Self {
        Self {
            reader,

            chunks: chunks.into_iter(),

            reference_sequence_name,
            interval,

            state: State::Seek,
            header,

            record: Record::default(),
        }
    }

    fn read_record(&mut self) -> io::Result<Option<Record>> {
        self.reader
            .read_record(self.header, &mut self.record)
            .map(|n| match n {
                0 => None,
                _ => Some(self.record.clone()),
            })
    }
}

impl<'r, 'h, R> Iterator for Query<'r, 'h, R>
where
    R: Read + Seek,
{
    type Item = io::Result<Record>;

    fn next(&mut self) -> Option<Self::Item> {
        loop {
            match self.state {
                State::Seek => {
                    self.state = match self.chunks.next() {
                        Some(chunk) => {
                            if let Err(e) = self.reader.seek(chunk.start()) {
                                return Some(Err(e));
                            }

                            State::Read(chunk.end())
                        }
                        None => State::Done,
                    }
                }
                State::Read(chunk_end) => match self.read_record() {
                    Ok(Some(record)) => {
                        if self.reader.virtual_position() >= chunk_end {
                            self.state = State::Seek;
                        }

                        match intersects(&record, &self.reference_sequence_name, self.interval) {
                            Ok(true) => return Some(Ok(record)),
                            Ok(false) => {}
                            Err(e) => return Some(Err(e)),
                        }
                    }
                    Ok(None) => self.state = State::Seek,
                    Err(e) => return Some(Err(e)),
                },
                State::Done => return None,
            }
        }
    }
}

pub(crate) fn intersects(
    record: &Record,
    reference_sequence_name: &str,
    region_interval: Interval,
) -> io::Result<bool> {
    use noodles_core::Position;

    let name = record.chromosome().to_string();

    let start = Position::try_from(usize::from(record.position()))
        .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;

    let end = record
        .end()
        .map(usize::from)
        .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
        .and_then(|n| {
            Position::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
        })?;

    let record_interval = Interval::from(start..=end);

    Ok(name == reference_sequence_name && record_interval.intersects(region_interval))
}