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(())
}
}