Struct Writer

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

An async CRAM writer.

A call to Self::shutdown must be made before the writer is dropped.

Implementations

impl<W> Writer<W>

where W: AsyncWrite + Unpin,

pub fn new(inner: W) -> Self

Creates an async CRAM writer.

Examples

use noodles_cram as cram;
use tokio::io;
let writer = cram::r#async::io::Writer::new(io::sink());

pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

Examples

use noodles_cram as cram;
use tokio::io;
let writer = cram::r#async::io::Writer::new(io::sink());
let inner = writer.get_ref();

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

Attempts to shutdown the output stream by writing any pending containers and a final EOF container.

Examples

use noodles_cram as cram;
use noodles_sam as sam;
use tokio::io;
let mut writer = cram::r#async::io::Writer::new(io::sink());
let header = sam::Header::default();
writer.shutdown(&header).await?;

pub async fn write_file_definition(&mut self) -> Result<()>

Writes a CRAM file definition.

The file ID is set as a blank value ([0x00; 20]).

Examples

use noodles_cram as cram;

let mut writer = cram::r#async::io::Writer::new(Vec::new());
writer.write_file_definition().await?;

assert_eq!(writer.get_ref(), &[
    // magic number (CRAM)
    0x43, 0x52, 0x41, 0x4d,
    // format (major, minor)
    0x03, 0x00,
    // file ID
    0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
    0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
]);

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

Writes a CRAM file header container.

The position of the stream is expected to be directly after the file definition.

Entries in the reference sequence dictionary that are missing MD5 checksums (M5) will automatically be calculated and added to the written record.

Examples

use noodles_cram as cram;
use noodles_sam as sam;
use tokio::io;

let mut writer = cram::r#async::io::Writer::new(io::sink());
writer.write_file_definition().await?;

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

writer.shutdown(&header).await?;

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

Writes a SAM header.

This writes the CRAM magic number, the file definition, and file header using the given SAM header.

use noodles_cram as cram;
use noodles_sam as sam;
use tokio::io;

let mut writer = cram::r#async::io::Writer::new(io::sink());

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

writer.shutdown(&header).await?;

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

Writes a CRAM record.

Examples

use noodles_cram as cram;
use noodles_sam as sam;
use tokio::io;

let mut writer = cram::r#async::io::Writer::new(io::sink());
writer.write_file_definition().await?;

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

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

writer.shutdown(&header).await?;

pub async fn write_alignment_record<R>( &mut self, header: &Header, record: &R, ) -> Result<()>

where R: Record + ?Sized,

Writes an alignment record.

Examples

use noodles_cram as cram;
use noodles_sam as sam;
use tokio::io;

let mut writer = cram::r#async::io::Writer::new(io::sink());
writer.write_file_definition().await?;

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

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

writer.shutdown(&header).await?;