Crate noodles_fastq

noodles-fastq handles the reading and writing of the FASTQ format.

FASTQ is a text format with no formal specification and only has de facto rules. It typically consists of a list of records, each with four lines: a read name, a sequence, a plus line, and quality scores.

The read name is prefixed with an @ (at sign) character. The sequence is a list of bases encoded using IUPAC base symbols. The plus line is effectively a separator, sometimes repeating the read name, and is commonly discarded. The quality scores is list of Phred quality scores offset by 33 and is parallel to a base in the sequence.

Examples

Read all records from a file

use noodles_fastq as fastq;

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

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

Modules

fai

FASTQ index (FAI) and fields.

Structs

AsyncReader

An async FASTQ reader.

AsyncWriter

An async FASTQ writer.

Indexer

A FASTQ indexer.

Reader

A FASTQ reader.

Record

A FASTQ record.

Writer

A FASTQ writer.

Functions

index

Indexes a FASTQ file.