Struct noodles::bcf::Writer

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

A BCF writer.

Implementations

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

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

Creates a BCF writer with a default compression level.

The given stream is wrapped in a BGZF encoder.

Examples

use noodles_bcf as bcf;
let writer = bcf::Writer::new(Vec::new());

pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

Examples

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

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

Attempts to finish the output stream.

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

Examples

use noodles_bcf as bcf;
let mut writer = bcf::Writer::new(Vec::new());
writer.try_finish()?;

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

Writes a BCF file format.

Examples

use noodles_bcf as bcf;
let mut writer = bcf::Writer::new(Vec::new());
writer.write_file_format()?;

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

Writes a VCF header.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

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

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

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

Writes a VCF record.

Examples

use noodles_bcf::{self as bcf, header::StringMap};
use noodles_vcf::{self as vcf, header::Contig, record::Position};

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

let header = vcf::Header::builder()
    .add_contig(Contig::new("sq0"))
    .build();

writer.write_header(&header)?;

let string_map = StringMap::from(&header);

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(8)?)
    .set_reference_bases("A".parse()?)
    .build()?;

writer.write_vcf_record(&header, &string_map, &record)?;