Struct noodles::bam::Writer

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

A BAM writer.

Since the raw text header and bam::Record are immutable, BAM files are created by encoding a SAM header and SAM records.

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

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

Implementations

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

pub fn new(writer: W) -> Writer<W>

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 get_ref(&self) -> &W

Returns a reference to the underlying writer.

Examples

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

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

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()?;

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

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: &IndexMap<String, ReferenceSequence, RandomState>
) -> Result<(), Error>

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", 8)?)
    .add_comment("noodles-bam")
    .build();

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

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

Writes a BAM record.

Examples

use noodles_bam as bam;
let mut writer = bam::Writer::new(Vec::new());
let record = bam::Record::default();
writer.write_record(&record)?;

pub fn write_sam_record(
    &mut self,
    reference_sequences: &IndexMap<String, ReferenceSequence, RandomState>,
    record: &Record
) -> Result<(), Error>

Writes a SAM record.

Examples

use noodles_bam as bam;
use noodles_sam as sam;

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

let reference_sequences = sam::header::ReferenceSequences::new();
let record = sam::Record::default();
writer.write_sam_record(&reference_sequences, &record)?;