Struct noodles_cram::io::writer::Writer

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

Expand description

A CRAM writer.

A call to Self::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::io::Writer::new(Vec::new());

let header = sam::Header::default();
writer.write_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 new(inner: W) -> Self

Creates a new CRAM writer with default options.

§Examples

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

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

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::io::Writer::new(Vec::new());
writer.try_finish(&header)?;

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pub 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::io::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<()>

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;

let mut writer = cram::io::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_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;

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

let header = sam::Header::builder().add_comment("noodles-cram").build();
writer.write_header(&header)?;

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pub 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;

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

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

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

writer.try_finish(&header)?;