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use std::io::{self, Write};
use super::{Header, Record};
/// A SAM writer.
///
/// 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
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
///
/// let mut writer = sam::Writer::new(Vec::new());
///
/// let header = sam::Header::builder().add_comment("noodles-sam").build();
/// writer.write_header(&header)?;
///
/// let record = sam::Record::default();
/// writer.write_record(&record)?;
///
/// let expected = b"@CO\tnoodles-sam
/// *\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
/// ";
///
/// assert_eq!(&writer.get_ref()[..], &expected[..]);
/// # Ok::<(), io::Error>(())
/// ```
pub struct Writer<W>
where
W: Write,
{
inner: W,
}
impl<W> Writer<W>
where
W: Write,
{
/// Creates a SAM writer.
///
/// # Examples
///
/// ```
/// use noodles_sam as sam;
/// let writer = sam::Writer::new(Vec::new());
/// ```
pub fn new(inner: W) -> Self {
Self { inner }
}
/// Returns a reference to the underlying writer.
///
/// # Examples
///
/// ```
/// use noodles_sam as sam;
/// let writer = sam::Writer::new(Vec::new());
/// assert!(writer.get_ref().is_empty());
/// ```
pub fn get_ref(&self) -> &W {
&self.inner
}
/// Returns the underlying writer.
///
/// # Examples
///
/// ```
/// use noodles_sam as sam;
/// let writer = sam::Writer::new(Vec::new());
/// assert!(writer.into_inner().is_empty());
/// ```
pub fn into_inner(self) -> W {
self.inner
}
/// Writes a SAM header.
///
/// The SAM header is optional, though recommended to include. A call to this method can be
/// omitted if it is empty.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
/// let mut writer = sam::Writer::new(Vec::new());
/// let header = sam::Header::builder().add_comment("noodles-sam").build();
/// writer.write_header(&header)?;
/// assert_eq!(writer.get_ref(), b"@CO\tnoodles-sam\n");
/// # Ok::<(), io::Error>(())
/// ```
pub fn write_header(&mut self, header: &Header) -> io::Result<()> {
write!(self.inner, "{}", header)
}
/// Writes a SAM record.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_sam as sam;
/// let mut writer = sam::Writer::new(Vec::new());
/// let record = sam::Record::default();
/// writer.write_record(&record)?;
/// assert_eq!(writer.get_ref(), b"*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*\n");
/// # Ok::<(), io::Error>(())
/// ```
pub fn write_record(&mut self, record: &Record) -> io::Result<()> {
writeln!(self.inner, "{}", record)
}
}
#[cfg(test)]
mod tests {
use std::convert::TryFrom;
use crate::record::{
data::{self, Field},
Data,
};
use super::*;
#[test]
fn test_write_record_with_data() -> Result<(), Box<dyn std::error::Error>> {
let mut writer = Writer::new(vec![]);
let data = Data::try_from(vec![Field::new(
data::field::Tag::ReadGroup,
data::field::Value::String(String::from("rg0")),
)])?;
let record = Record::builder().set_data(data).build()?;
writer.write_record(&record)?;
let expected = b"*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*\tRG:Z:rg0\n";
assert_eq!(&writer.get_ref()[..], &expected[..]);
Ok(())
}
}