fastq

Documentation

Overview

Package fastq decodes and encodes fastq files.

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) MarshalText() ([]byte, error)
• type Reader
  • func NewReader(r io.Reader) *Reader
  • func (r *Reader) Read() (*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) MarshalText

func (f *Fastq) MarshalText() ([]byte, error)

MarshalText 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) Read

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

Read 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.