Struct noodles::cram::Writer

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

Expand description

A CRAM writer.

A call to [try_finish] must be made before the writer is dropped.

Examples

use noodles_cram as cram;
use noodles_sam as sam;

let mut writer = cram::Writer::builder(Vec::new()).build();
writer.write_file_definition()?;

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

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

writer.try_finish(&header)?;

Implementations

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

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pub fn builder(inner: W) -> Builder<W>

Creates a CRAM writer builder.

Examples

use noodles_cram as cram;
let builder = cram::Writer::builder(Vec::new());
let writer = builder.build();

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

Creates a new CRAM writer with default options.

Examples

use noodles_cram as cram;
let writer = cram::Writer::new(Vec::new());

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pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

Examples

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

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

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

This is typically only manually called if the underlying stream is needed before the writer is dropped.

Examples

use noodles_cram as cram;
use noodles_sam as sam;

let header = sam::Header::default();
let mut writer = cram::Writer::new(Vec::new());
writer.try_finish(&header)?;

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

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

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,
]);

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

Writes a CRAM file header container.

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

Reference sequence dictionary entries must have MD5 checksums (M5) set.

Examples

use noodles_cram as cram;
use noodles_sam as sam;

let mut writer = cram::Writer::new(Vec::new());
writer.write_file_definition()?;

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

writer.try_finish(&header)?;

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

Writes a CRAM record.

Examples

use noodles_cram as cram;
use noodles_sam as sam;


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

writer.write_file_definition()?;

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

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

writer.try_finish(&header)?;