Struct Reader

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

A FASTQ reader.

Implementations

impl<R> Reader<R>

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

Examples

use noodles_fastq as fastq;
let reader = fastq::io::Reader::new(io::empty());
let _inner = reader.get_ref();

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

Returns a mutable reference to the underlying reader.

Examples

use noodles_fastq as fastq;
let mut reader = fastq::io::Reader::new(io::empty());
let _inner = reader.get_mut();

pub fn into_inner(self) -> R

Unwraps and returns the underlying reader.

Examples

use noodles_fastq as fastq;
let reader = fastq::io::Reader::new(io::empty());
let _inner = reader.into_inner();

impl<R> Reader<R>

where R: BufRead,

pub fn new(inner: R) -> Self

Creates a FASTQ reader.

Examples

use noodles_fastq as fastq;
let data = b"@r0\nATCG\n+\nNDLS\n";
let reader = fastq::io::Reader::new(&data[..]);

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

Reads a FASTQ record.

This reads from the underlying stream until four lines are read: the read name, the sequence, the plus line, and the quality scores. Each line omits the trailing newline.

The stream is expected to be at the start of a record.

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

Examples

use noodles_fastq as fastq;

let data = b"@r0\nATCG\n+\nNDLS\n";
let mut reader = fastq::io::Reader::new(&data[..]);

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

assert_eq!(record.name(), &b"r0"[..]);
assert_eq!(record.sequence(), b"ATCG");
assert_eq!(record.quality_scores(), b"NDLS");
Ok::<(), io::Error>(())

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

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

The stream is expected to be at the start of a record.

Examples

use noodles_fastq::{self as fastq, record::Definition};

let data = b"@r0\nATCG\n+\nNDLS\n";
let mut reader = fastq::io::Reader::new(&data[..]);

let mut records = reader.records();

assert_eq!(
    records.next().transpose()?,
    Some(fastq::Record::new(Definition::new("r0", ""), "ATCG", "NDLS")
));

assert!(records.next().is_none());