Struct noodles::cram::Writer

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

A CRAM writer.

Examples

use noodles_cram as cram;
use noodles_sam as sam;

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

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

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

Implementations

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

pub fn new(inner: W, reference_sequences: Vec<Record, Global>) -> Writer<W>

Creates a new CRAM writer.

Examples

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

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(), Vec::new());
assert!(writer.get_ref().is_empty());

pub fn try_finish(&mut self) -> 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;
let mut writer = cram::Writer::new(Vec::new(), Vec::new());
writer.try_finish()?;

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(), 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,
]);

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

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

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

Writes a CRAM record.

Examples

use noodles_cram as cram;
let mut writer = cram::Writer::new(Vec::new(), Vec::new());
let record = cram::Record::default();
writer.write_record(record)?;

Trait Implementations

impl<W> Debug for Writer<W> where
    W: Debug + Write, 

pub fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

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

pub fn drop(&mut self)

Executes the destructor for this type.