Struct Writer

Source

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

Expand description

A VCF writer.

§Examples

use noodles_core::Position;
use noodles_vcf::{
    self as vcf,
    header::{
        record::value::{map::Contig, Map},
        FileFormat,
    },
    variant::io::Write,
};

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

let header = vcf::Header::builder()
    .set_file_format(FileFormat::new(4, 5))
    .add_contig("sq0", Map::<Contig>::new())
    .build();

writer.write_header(&header)?;

let record = vcf::variant::RecordBuf::builder()
    .set_reference_sequence_name("sq0")
    .set_variant_start(Position::MIN)
    .set_reference_bases("A")
    .build();

writer.write_variant_record(&header, &record);

let expected = b"##fileformat=VCFv4.5
##contig=<ID=sq0>
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
sq0\t1\t.\tA\t.\t.\t.\t.
";

assert_eq!(&writer.get_ref()[..], &expected[..]);

Implementations§

Source §

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

Source

pub fn new(inner: W) -> Self

Creates a VCF writer.

§Examples

use noodles_vcf as vcf;
let writer = vcf::io::Writer::new(Vec::new());

Source

pub fn get_ref(&self) -> &W

Returns a reference to the underlying writer.

§Examples

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

Source

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

Returns a mutable reference to the underlying writer.

§Examples

use noodles_vcf as vcf;
let mut writer = vcf::io::Writer::new(Vec::new());
assert!(writer.get_mut().is_empty());

Source

pub fn into_inner(self) -> W

Unwraps and returns the underlying writer.

§Examples

use noodles_vcf as vcf;
let writer = vcf::io::Writer::new(Vec::new());
assert!(writer.into_inner().is_empty());

Source

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

Writes a VCF header.

§Examples

use noodles_vcf as vcf;

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

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

Source

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

Writes a VCF record.

§Examples

use noodles_core::Position;
use noodles_vcf as vcf;

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

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

assert_eq!(writer.get_ref(), b"sq0\t1\t.\tA\t.\t.\t.\t.\n");