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//! SAM reader and iterators.
mod records;
pub use self::records::Records;
use std::io::{self, BufRead, Read, Seek};
use noodles_bgzf as bgzf;
const LINE_FEED: char = '\n';
const CARRIAGE_RETURN: char = '\r';
const HEADER_PREFIX: u8 = b'@';
/// A SAM reader.
///
/// The SAM format is comprised of two parts: 1) a header and 2) a list of records.
///
/// Each header line is prefixed with an `@` (at sign). The header is optional and may be empty.
///
/// SAM records are line-based and follow directly after the header or the start of the file until
/// EOF.
///
/// # Examples
///
/// ```no_run
/// # use std::{fs::File, io::{self, BufReader}};
/// use noodles_sam as sam;
///
/// let mut reader = File::open("sample.sam")
/// .map(BufReader::new)
/// .map(sam::Reader::new)?;
///
/// reader.read_header()?;
///
/// for result in reader.records() {
/// let record = result?;
/// println!("{:?}", record);
/// }
/// # Ok::<(), io::Error>(())
/// ```
#[derive(Debug)]
pub struct Reader<R> {
inner: R,
}
impl<R> Reader<R>
where
R: BufRead,
{
/// Creates a SAM reader.
///
/// # Examples
///
/// ```
/// use noodles_sam as sam;
///
/// let data = b"@HD\tVN:1.6
/// *\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
/// ";
///
/// let reader = sam::Reader::new(&data[..]);
/// ```
pub fn new(inner: R) -> Self {
Self { inner }
}
/// Returns the underlying reader.
///
/// # Examples
///
/// ```
/// use noodles_sam as sam;
/// let data = [];
/// let reader = sam::Reader::new(&data[..]);
/// assert!(reader.into_inner().is_empty());
/// ```
pub fn into_inner(self) -> R {
self.inner
}
/// Reads the raw SAM header.
///
/// The position of the stream is expected to be at the start.
///
/// This returns the raw SAM header as a [`String`]. It can subsequently be parsed as a
/// [`crate::Header`].
///
/// The SAM header is optional, and if it is missing, an empty string is returned.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
///
/// let data = b"@HD\tVN:1.6
/// *\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
/// ";
///
/// let mut reader = sam::Reader::new(&data[..]);
/// let header = reader.read_header()?;
///
/// assert_eq!(header, "@HD\tVN:1.6\n");
/// # Ok::<(), io::Error>(())
/// ```
pub fn read_header(&mut self) -> io::Result<String> {
read_header(&mut self.inner)
}
/// Reads a single raw SAM record.
///
/// This reads from the underlying stream until a newline is reached and appends it to the
/// given buffer, sans the final newline character.
///
/// The stream is expected to be directly after the header or at the start of another record.
///
/// It is more ergonomic to read records using an iterator (see [`Self::records`]), but using
/// this method allows control of the line buffer and whether the raw record should be parsed.
///
/// If successful, the number of bytes read is returned. If the number of bytes read is 0, the
/// stream reached EOF.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
///
/// let data = b"@HD\tVN:1.6
/// *\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
/// ";
///
/// let mut reader = sam::Reader::new(&data[..]);
/// reader.read_header()?;
///
/// let mut buf = String::new();
/// reader.read_record(&mut buf)?;
/// assert_eq!(buf, "*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*");
///
/// assert_eq!(reader.read_record(&mut buf)?, 0);
/// # Ok::<(), io::Error>(())
/// ```
pub fn read_record(&mut self, buf: &mut String) -> io::Result<usize> {
read_line(&mut self.inner, buf)
}
/// Returns an iterator over records starting from the current stream position.
///
/// The stream is expected to be directly after the header or at the start of another record.
///
/// Unlike [`Self::read_record`], each record is parsed as a [`crate::Record`].
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
///
/// let data = b"@HD\tVN:1.6
/// *\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
/// ";
///
/// let mut reader = sam::Reader::new(&data[..]);
/// reader.read_header()?;
///
/// let mut records = reader.records();
/// assert!(records.next().is_some());
/// assert!(records.next().is_none());
/// # Ok::<(), io::Error>(())
/// ```
pub fn records(&mut self) -> Records<'_, R> {
Records::new(self)
}
}
impl<R> Reader<bgzf::Reader<R>>
where
R: Read + Seek,
{
/// Seeks the underlying BGZF stream to the given virtual position.
///
/// Virtual positions typically come from an associated index.
///
/// # Examples
///
/// ```no_run
/// # use std::{fs::File, io};
/// use std::io::BufReader;
///
/// use noodles_bgzf as bgzf;
/// use noodles_sam as sam;
///
/// let mut reader = File::open("sample.sam.gz")
/// .map(bgzf::Reader::new)
/// .map(sam::Reader::new)?;
///
/// let virtual_position = bgzf::VirtualPosition::from(102334155);
/// reader.seek(virtual_position)?;
/// # Ok::<(), io::Error>(())
/// ```
pub fn seek(&mut self, pos: bgzf::VirtualPosition) -> io::Result<bgzf::VirtualPosition> {
self.inner.seek(pos)
}
}
fn read_header<R>(reader: &mut R) -> io::Result<String>
where
R: BufRead,
{
let mut header_buf = Vec::new();
let mut is_eol = false;
for i in 0.. {
let buf = reader.fill_buf()?;
if (i == 0 || is_eol) && buf.first().map(|&b| b != HEADER_PREFIX).unwrap_or(true) {
break;
}
let (read_eol, len) = if let Some(i) = buf.iter().position(|&b| b == LINE_FEED as u8) {
header_buf.extend(&buf[..=i]);
(true, i + 1)
} else {
header_buf.extend(buf);
(false, buf.len())
};
is_eol = read_eol;
reader.consume(len);
}
String::from_utf8(header_buf).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
}
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 std::io::BufReader;
use super::*;
#[test]
fn test_read_header_with_no_header() -> io::Result<()> {
let data = b"*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*\n";
let mut reader = &data[..];
assert!(read_header(&mut reader)?.is_empty());
Ok(())
}
#[test]
fn test_read_header_with_no_records() -> io::Result<()> {
let data = "@HD\tVN:1.6\n";
let mut reader = data.as_bytes();
let header = read_header(&mut reader)?;
assert_eq!(header, data);
Ok(())
}
#[test]
fn test_read_header_with_multiple_buffer_fills() -> io::Result<()> {
let data = "@HD\tVN:1.6\n@SQ\tSN:sq0\tLN:8\n";
let mut reader = BufReader::with_capacity(16, data.as_bytes());
let header = read_header(&mut reader)?;
assert_eq!(header, data);
Ok(())
}
#[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(())
}
}