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
148
149
150
151
152
153
use std::io::{self, BufRead};

/// A FASTQ index reader.
#[derive(Debug)]
pub struct Reader<R> {
    inner: R,
}

impl<R> Reader<R> {
    /// Returns a reference to the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq::fai;
    /// let reader = fai::Reader::new(io::empty());
    /// let _inner = reader.get_ref();
    /// ```
    pub fn get_ref(&self) -> &R {
        &self.inner
    }

    /// Returns a mutable reference to the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq::fai;
    /// let mut reader = fai::Reader::new(io::empty());
    /// let _inner = reader.get_mut();
    /// ```
    pub fn get_mut(&mut self) -> &mut R {
        &mut self.inner
    }

    /// Returns the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq::fai;
    /// let reader = fai::Reader::new(io::empty());
    /// let _inner = reader.into_inner();
    /// ```
    pub fn into_inner(self) -> R {
        self.inner
    }
}

impl<R> Reader<R>
where
    R: BufRead,
{
    /// Creates a FASTQ index reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_fastq::fai;
    /// let data = b"r0\t4\t4\t4\t5\t11\n";
    /// let mut reader = fai::Reader::new(&data[..]);
    /// ```
    pub fn new(inner: R) -> Self {
        Self { inner }
    }

    /// Reads a raw FASTQ index record.
    ///
    /// The given buffer will not include the trailing newline. It can subsequently be parsed as a
    /// [`super::Record`].
    ///
    /// The position of the stream is expected to be at the start or at the start of another
    /// record.
    ///
    /// If successful, this returns the number of bytes read from the stream. If the number of
    /// bytes read is 0, the stream reached EOF.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fastq::fai;
    ///
    /// let data = b"r0\t4\t4\t4\t5\t11\n";
    /// let mut reader = fai::Reader::new(&data[..]);
    ///
    /// let mut buf = String::new();
    /// reader.read_record(&mut buf)?;
    ///
    /// assert_eq!(buf, "r0\t4\t4\t4\t5\t11");
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn read_record(&mut self, buf: &mut String) -> io::Result<usize> {
        read_line(&mut self.inner, buf)
    }
}

fn read_line<R>(reader: &mut R, buf: &mut String) -> io::Result<usize>
where
    R: BufRead,
{
    const LINE_FEED: char = '\n';
    const CARRIAGE_RETURN: char = '\r';

    match reader.read_line(buf) {
        Ok(0) => Ok(0),
        Ok(n) => {
            if buf.ends_with(LINE_FEED) {
                buf.pop();

                if buf.ends_with(CARRIAGE_RETURN) {
                    buf.pop();
                }
            }

            Ok(n)
        }
        Err(e) => Err(e),
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_read_line() -> io::Result<()> {
        let mut buf = String::new();

        let data = b"noodles\n";
        let mut reader = &data[..];
        buf.clear();
        read_line(&mut reader, &mut buf)?;
        assert_eq!(buf, "noodles");

        let data = b"noodles\r\n";
        let mut reader = &data[..];
        buf.clear();
        read_line(&mut reader, &mut buf)?;
        assert_eq!(buf, "noodles");

        let data = b"noodles";
        let mut reader = &data[..];
        buf.clear();
        read_line(&mut reader, &mut buf)?;
        assert_eq!(buf, "noodles");

        Ok(())
    }
}