Struct noodles_sam::io::writer::Writer

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pub struct Writer<W>where
    W: Write,
{ /* private fields */ }

Expand description

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 noodles_sam as sam;

let mut writer = sam::io::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(&header, &record)?;

let expected = b"@CO\tnoodles-sam
*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*
";

assert_eq!(&writer.get_ref()[..], &expected[..]);

Implementations§

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impl<W> Writer<W>
where W: Write,

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pub fn new(inner: W) -> Self

Creates a SAM writer.

§Examples

use noodles_sam as sam;
let writer = sam::io::Writer::new(Vec::new());

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pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

§Examples

use noodles_sam as sam;
let writer = sam::io::Writer::new(Vec::new());
assert!(writer.get_ref().is_empty());

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pub fn get_mut(&mut self) -> &mut W

Returns a mutable reference to the underlying writer.

§Examples

use noodles_sam as sam;
let mut writer = sam::io::Writer::new(Vec::new());
assert!(writer.get_mut().is_empty());

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pub fn into_inner(self) -> W

Returns the underlying writer.

§Examples

use noodles_sam as sam;
let writer = sam::io::Writer::new(Vec::new());
assert!(writer.into_inner().is_empty());

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pub fn write_header(&mut self, header: &Header) -> Result<()>

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 noodles_sam as sam;
let mut writer = sam::io::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");

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pub fn write_record(&mut self, header: &Header, record: &Record) -> Result<()>

Writes a SAM record.

§Examples

use noodles_sam as sam;

let mut writer = sam::io::Writer::new(Vec::new());

let header = sam::Header::default();
let record = sam::Record::default();
writer.write_record(&header, &record)?;

assert_eq!(writer.get_ref(), b"*\t4\t*\t0\t255\t*\t*\t0\t0\t*\t*\n");