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

const LINE_FEED: char = '\n';
const CARRIAGE_RETURN: char = '\r';

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

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,
{
    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(())
    }
}