Struct noodles_bam::writer::Writer

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

A BAM writer.

Examples

use noodles_bam as bam;
use noodles_sam::{self as sam, alignment::Record};

let mut writer = bam::Writer::new(Vec::new());

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

let record = 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::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::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::Writer::from(Vec::new());
assert!(writer.into_inner().is_empty());

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

Writes a SAM header.

Examples

use noodles_bam as bam;
use noodles_sam as sam;

let mut writer = bam::Writer::new(Vec::new());

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

pub fn write_reference_sequences(
    &mut self,
    reference_sequences: &ReferenceSequences
) -> Result<()>

Writes SAM reference sequences.

The reference sequences here are typically the same as the reference sequences in the SAM header.

Examples

use noodles_bam as bam;
use noodles_sam::{self as sam, header::ReferenceSequence};

let mut writer = bam::Writer::new(Vec::new());

let header = sam::Header::builder()
    .add_reference_sequence(ReferenceSequence::new("sq0".parse()?, 8)?)
    .add_comment("noodles-bam")
    .build();

writer.write_header(&header)?;
writer.write_reference_sequences(header.reference_sequences())?;

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

Writes a BAM record.

Examples

use noodles_bam as bam;
use noodles_sam::{self as sam, alignment::Record};

let mut writer = bam::Writer::new(Vec::new());

let header = sam::Header::default();
let record = 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::Writer::new(Vec::new());

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::Writer::new(Vec::new());
writer.try_finish()?;

Trait Implementations

impl<W> AlignmentWriter 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: &Record
) -> Result<()>

Writes an alignment record.

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

Shuts down an alignment format writer.

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

fn from(inner: W) -> Self

Converts to this type from the input type.