Struct noodles_bcf::Reader

pub struct Reader<R> { /* fields omitted */ }

A BCF reader.

The BCF format is comprised of two parts: 1) a VCF header and 2) a list of records.

Implementations

impl<R> Reader<R> where
    R: Read, 

pub fn new(reader: R) -> Self

Creates a BCF reader.

Examples

use noodles_bcf as bcf;
let data = [];
let reader = bcf::Reader::new(&data[..]);

pub fn read_file_format(&mut self) -> Result<(u8, u8)>

Reads the BCF file format.

The BCF magic number is also checked.

The position of the stream is expected to be at the start.

This returns the major and minor format versions as a tuple.

Examples

use noodles_bcf as bcf;
let mut reader = File::open("sample.bcf").map(bcf::Reader::new)?;
let (major, minor) = reader.read_file_format()?;

pub fn read_header(&mut self) -> Result<String>

Reads the raw VCF header.

The position of the stream is expected to be directly after the file format.

This returns the raw VCF header as a String. It can subsequently be parsed as a noodles_vcf::Header.

Examples

use noodles_bcf as bcf;
let mut reader = File::open("sample.bcf").map(bcf::Reader::new)?;
reader.read_file_format()?;
let header = reader.read_header()?;

pub fn read_record(&mut self, record: &mut Record) -> Result<usize>

Reads a single record.

The stream is expected to be directly after the header or at the start of another record.

It is more ergnomic to read records using an iterator (see Self::records), but using this method directly allows the reuse of a single Record buffer.

If successful, the record size is returned. If a record size of 0 is returned, the stream reached EOF.

Examples

use noodles_bcf as bcf;

let mut reader = File::open("sample.bcf").map(bcf::Reader::new)?;
reader.read_file_format()?;
reader.read_header()?;

let mut record = bcf::Record::default();
reader.read_record(&mut record)?;

pub fn records(&mut self) -> Records<'_, R>

Returns an iterator over records starting from the current stream position.

The stream is expected to be directly after the header or at the start of another record.

Examples

use noodles_bcf as bcf;

let mut reader = File::open("sample.bcf").map(bcf::Reader::new)?;
reader.read_file_format()?;
reader.read_header()?;

for result in reader.records() {
    let record = result?;
    println!("{:?}", &record[..]);
}

pub fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position of the underlying BGZF reader.

Examples

use noodles_bcf as bcf;

let data = Vec::new();
let reader = bcf::Reader::new(&data[..]);
let virtual_position = reader.virtual_position();

assert_eq!(virtual_position.compressed(), 0);
assert_eq!(virtual_position.uncompressed(), 0);

impl<R> Reader<R> where
    R: Read + Seek, 

pub fn seek(&mut self, pos: VirtualPosition) -> Result<VirtualPosition>

Seeks the underlying BGZF reader to the given virtual position.

Virtual positions typically come from an associated BCF index file.

Examples

use noodles_bcf as bcf;
use noodles_bgzf as bgzf;

let mut reader = File::open("sample.bcf").map(bcf::Reader::new)?;

let virtual_position = bgzf::VirtualPosition::from(102334155);
reader.seek(virtual_position)?;

pub fn query<I, IRS>(
    &mut self,
    contigs: &Contigs,
    index: &I,
    region: &Region
) -> Result<Query<'_, R>> where
    I: BinningIndex<IRS>,
    IRS: BinningIndexReferenceSequence, 

Returns an iterator over records that intersects the given region.

Examples

use noodles_bcf as bcf;
use noodles_core::Region;
use noodles_csi as csi;
use noodles_vcf as vcf;

let mut reader = File::open("sample.bcf").map(bcf::Reader::new)?;

let header: vcf::Header = reader.read_header()?.parse()?;
let contigs = header.contigs();

let index = csi::read("sample.bcf.csi")?;
let region = Region::mapped("sq0", 8..=13);
let query = reader.query(&contigs, &index, &region)?;

for result in query {
    let record = result?;
    // ...
}