Struct bam::sam::SamWriter

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

Writes records in SAM format.

Can be created as

let writer = SamWriter::from_path("out.sam", header).unwrap();

or using a builder

let writer = SamWriter::build()
    .write_header(false)
    .from_path("out.sam", header).unwrap();

You can clone a header from SAM/BAM reader or create one yourself.

You need to import RecordWriter to write records:

use bam::RecordWriter;
let mut writer = bam::SamWriter::from_path("out.sam", header).unwrap();
let mut record = bam::Record::new();
// Filling the record.
writer.write(&record).unwrap();

Implementations

impl SamWriter<BufWriter<File>>

pub fn build() -> SamWriterBuilder

Create a builder.

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

Creates a SAM writer from a path and a header.

impl<W: Write> SamWriter<W>

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

Creates a SAM writer from a stream and a header. Preferably the stream should be wrapped in a buffer writer, such as BufWriter.

pub fn header(&self) -> &Header

Returns header.

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

Flushes contents to output.

pub fn take_stream(self) -> W

Consumes the writer and returns inner stream.

Trait Implementations

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

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

Writes a single record in SAM format.

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.