Struct noodles_vcf::reader::Reader

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

A VCF reader.

The VCF format has two main parts: 1) a header and 2) a list of VCF records.

Each header line is prefixed with a # (number sign) and is terminated by the header header (#CHROM…; inclusive).

VCF records are line-based and follow directly after the header until EOF.

Examples

use noodles_vcf as vcf;

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

let header = reader.read_header()?.parse()?;

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

Implementations

impl<R> Reader<R> where
    R: BufRead, 

pub fn new(inner: R) -> Self

Creates a VCF reader.

Examples

use noodles_vcf as vcf;

let data = b"##fileformat=VCFv4.3
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
sq0\t1\t.\tA\t.\t.\tPASS\t.
";

let reader = vcf::Reader::new(&data[..]);

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_vcf as vcf;
let data = [];
let reader = vcf::Reader::new(&data[..]);
assert!(reader.get_ref().is_empty());

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

Returns a mutable reference to the underlying reader.

Examples

use noodles_vcf as vcf;
let data = [];
let mut reader = vcf::Reader::new(&data[..]);
assert!(reader.get_mut().is_empty());

pub fn into_inner(self) -> R

Unwraps and returns the underlying writer.

Examples

use noodles_vcf as vcf;
let data = [];
let reader = vcf::Reader::new(&data[..]);
assert!(reader.into_inner().is_empty());

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

Reads the raw VCF header.

This reads all header lines prefixed with a # (number sign), which includes the header header (#CHROM…).

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

This returns the raw VCF header as a String, and as such, it is not necessarily valid. The raw header can subsequently be parsed as a crate::Header.

Examples

use noodles_vcf as vcf;

let data = b"##fileformat=VCFv4.3
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
sq0\t1\t.\tA\t.\t.\tPASS\t.
";

let mut reader = vcf::Reader::new(&data[..]);
let header = reader.read_header()?;

assert_eq!(header, "##fileformat=VCFv4.3\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n");

pub fn read_record(&mut self, buf: &mut String) -> Result<usize>

Reads a single raw VCF record.

This reads from the underlying stream until a newline is reached and appends it to the given buffer, sans the final newline character. The buffer can subsequently be parsed as a crate::Record.

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

It is more ergonomic to read records using an iterator (see Self::records), but using this method allows control of the line buffer and whether the raw record should be parsed.

If successful, the number of bytes read is returned. If the number of bytes read is 0, the stream reached EOF.

Examples

use noodles_vcf as vcf;

let data = b"##fileformat=VCFv4.3
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
sq0\t1\t.\tA\t.\t.\tPASS\t.
";

let mut reader = vcf::Reader::new(&data[..]);
reader.read_header()?;

let mut buf = String::new();
reader.read_record(&mut buf)?;

assert_eq!(buf, "sq0\t1\t.\tA\t.\t.\tPASS\t.");

pub fn records<'r, 'h>(&'r mut self, header: &'h Header) -> Records<'r, 'h, 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.

Unlike Self::read_record, each record is parsed as a crate::Record.

Examples

use noodles_vcf as vcf;

let data = b"##fileformat=VCFv4.3
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
sq0\t1\t.\tA\t.\t.\tPASS\t.
";

let mut reader = vcf::Reader::new(&data[..]);
let header = reader.read_header()?.parse()?;

let mut records = reader.records(&header);
assert!(records.next().is_some());
assert!(records.next().is_none());

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

pub fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position of the underlying BGZF reader.

Examples

use noodles_bgzf as bgzf;
use noodles_vcf as vcf;

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

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

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

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

Seeks the underlying BGZF stream to the given virtual position.

Virtual positions typically come from an associated index.

Examples

use noodles_bgzf as bgzf;
use noodles_vcf as vcf;

let data = Cursor::new(Vec::new());
let mut reader = vcf::Reader::new(bgzf::Reader::new(data));

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

pub fn query<'r, 'h>(
    &'r mut self,
    header: &'h Header,
    index: &Index,
    region: &Region
) -> Result<Query<'r, 'h, R>>

Returns an iterator over records that intersects the given region.

Examples

use noodles_bgzf as bgzf;;
use noodles_core::Region;
use noodles_tabix as tabix;
use noodles_vcf as vcf;

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

let header = reader.read_header()?.parse()?;

let index = tabix::read("sample.vcf.gz.tbi")?;
let region = Region::mapped("sq0", 8..=13);
let query = reader.query(&header, &index, &region)?;

for result in query {
    let record = result?;
    println!("{:?}", record);
}
Ok::<_, Box<dyn std::error::Error>>(())

Trait Implementations

impl<R: Debug> Debug for Reader<R>

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

Formats the value using the given formatter.