Struct noodles_bcf::io::writer::Writer

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

A BCF writer.

Implementations

impl<W> Writer<W>

where W: Write,

pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

Examples

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

pub fn get_mut(&mut self) -> &mut W

Returns a mutable reference to the underlying writer.

Examples

use noodles_bcf as bcf;
let mut writer = bcf::io::Writer::from(Vec::new());
assert!(writer.get_mut().is_empty());

pub fn into_inner(self) -> W

Returns the underlying writer.

Examples

use noodles_bcf as bcf;
let mut writer = bcf::io::Writer::from(Vec::new());
assert!(writer.into_inner().is_empty());

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

Writes a VCF header.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

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

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

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

Writes a record.

Examples

use noodles_bcf as bcf;
use noodles_core::Position;
use noodles_vcf::{
    self as vcf,
    header::{
        record::value::{map::Contig, Map},
        StringMaps,
    },
};

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

let mut header = vcf::Header::builder()
    .add_contig("sq0", Map::<Contig>::new())
    .build();
*header.string_maps_mut() = StringMaps::try_from(&header)?;

writer.write_header(&header)?;

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

impl<W> Writer<Writer<W>>

where W: Write,

pub fn new(writer: W) -> Self

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::io::Writer::new(io::sink());

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

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::io::Writer::new(io::sink());
writer.try_finish()?;

Trait Implementations

impl<W> From<W> for Writer<W>

fn from(inner: W) -> Self

Converts to this type from the input type.

impl<W> Write for Writer<W>

where W: Write,

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

Writes a VCF header.

fn write_variant_record( &mut self, header: &Header, record: &dyn Record, ) -> Result<()>

Writes a variant record.