Struct bam::bam_writer::BamWriter

pub struct BamWriter<W: Write> { /* fields omitted */ }

Bam writer. Can be created using from_path or using BamWriterBuilder.

Use RecordWriter trait to write records.

Implementations

impl BamWriter<File>

pub fn build() -> BamWriterBuilder

Creates a BamWriterBuilder.

pub fn from_path<P: AsRef<Path>>(path: P, header: Header) -> Result<Self>

Creates a new BamWriter from a path and header.

impl<W: Write> BamWriter<W>

pub fn from_stream(stream: W, header: Header) -> Result<Self>

Creates a new BamWriter from a stream and header.

pub fn header(&self) -> &Header

Returns BAM header.

pub fn take_stream(self) -> W

Consumes the writer and returns inner stream.

pub fn pause(&mut self)

Pauses multi-thread writer until the next write operation. Does nothing to a single-thread writer.

Use with caution: pausing and unpausing takes some time. Additionally, blocks that are compressed at the moment will finish compressing, but will not be written. All other blocks in the queue will not be compressed nor written.

To compress and write all remaining blocks you can call flush before calling pause.

Trait Implementations

impl<W: Write> RecordWriter for BamWriter<W>

fn write(&mut self, record: &Record) -> Result<()>

Writes a single record.

fn finish(&mut self) -> Result<()>

Finishes the stream, same as std::mem::drop(writer), but can return an error.

fn flush(&mut self) -> Result<()>

Flushes contents.