fastq

Documentation

Overview

Package fastq handles fastq I/O.

This package uses the format described in: https://en.wikipedia.org/wiki/FASTQ_format

This package does not validate sequence and quality characters.

Index

• type Fastq
  • func (f *Fastq) Text() []byte
• type Reader
  • func NewReader(r io.Reader) *Reader
  • func (r *Reader) Next() (*Fastq, error)

Types

type Fastq

type Fastq struct {
	Name     []byte // Entry name (without the '@')
	Sequence []byte // Sequence as received
	Quals    []byte // Qualities as received
}

Fastq is a single sequence in a fastq file.

func (*Fastq) Text

func (f *Fastq) Text() []byte

Text returns the textual representation of f in fastq format. Includes a trailing new line.

type Reader

type Reader struct {
	// contains filtered or unexported fields
}

A Reader reads sequences from a fastq stream.

func NewReader

func NewReader(r io.Reader) *Reader

NewReader returns a new fastq reader that reads from r.

func (*Reader) Next

func (r *Reader) Next() (*Fastq, error)

Next reads the next fastq entry from the reader. Returns a non-nil error if reading fails, or io.EOF if encountered end of file. When EOF is returned, no fastq is available.