Struct noodles_bam::io::writer::Writer

pub struct Writer<W> { /* private fields */ }

A BAM writer.

Examples

use noodles_bam as bam;
use noodles_sam as sam;

let mut writer = bam::io::Writer::new(io::sink());

let header = sam::Header::default();
writer.write_header(&header)?;

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

Implementations

impl<W> Writer<W>

where W: Write,

pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

Examples

use noodles_bam as bam;
let writer = bam::io::Writer::from(Vec::new());
assert!(writer.get_ref().is_empty());

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

Returns a mutable reference to the underlying writer.

Examples

use noodles_bam as bam;
let mut writer = bam::io::Writer::from(Vec::new());
assert!(writer.get_mut().is_empty());

pub fn into_inner(self) -> W

Returns the underlying writer.

Examples

use noodles_bam as bam;
let writer = bam::io::Writer::from(Vec::new());
assert!(writer.into_inner().is_empty());

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

Writes a SAM header.

This writes the BAM magic number, the raw SAM header, and a copy of the reference sequence dictionary as binary reference sequences.

Examples

use noodles_bam as bam;
use noodles_sam as sam;

let mut writer = bam::io::Writer::new(io::sink());

let header = sam::Header::builder().add_comment("noodles-bam").build();
writer.write_header(&header)?;

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

Writes a BAM record.

Examples

use noodles_bam as bam;
use noodles_sam as sam;

let header = sam::Header::default();

let mut writer = bam::io::Writer::new(io::sink());
writer.write_header(&header)?;

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

impl<W> Writer<Writer<W>>

where W: Write,

pub fn new(writer: W) -> Self

Creates a BAM writer with a default compression level.

The given stream is wrapped in a BGZF encoder.

Examples

use noodles_bam as bam;
let writer = bam::io::Writer::new(io::sink());

pub fn try_finish(&mut self) -> Result<()>

Attempts to finish the output stream.

This is typically only manually called if the underlying stream is needed before the writer is dropped.

Examples

use noodles_bam as bam;
let mut writer = bam::io::Writer::new(io::sink());
writer.try_finish()?;

Trait Implementations

impl<W> From<W> for Writer<W>

fn from(inner: W) -> Self

Converts to this type from the input type.

impl<W> Write for Writer<W>

where W: Write,

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

Writes a SAM header.

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

Writes an alignment record.

fn finish(&mut self, _: &Header) -> Result<()>

Shuts down an alignment writer.