The FastQ format. (tag) More...

#include <seqan3/io/sequence_file/format_fastq.hpp>

Inheritance diagram for seqan3::format_fastq:

Static Public Attributes
static std::vector< std::string >	file_extensions
	The valid file extensions for this format; note that you can modify this value. More...

Detailed Description

The FastQ format. (tag)

Introduction

FastQ is the de-facto-standard for storing sequences together with quality information. See the article on wikipedia for a an in-depth description of the format.

Fields

The FastQ format provides the fields seqan3::field::SEQ, seqan3::field::ID and seqan3::field::QUAL; or alternatively provides seqan3::field::SEQ_QUAL as a single field of sequence and quality. All three fields (or ID + SEQ_QUAL) are required when writing and the sequence and qualities are required to be of the same length.

Encodings

All documented encodings for the quality string are supported (see the article above), but they are not detected from the file. Instead, when reading the file, you have to set the respective alphabet via a traits type (see seqan3::SequenceFileInputTraits and the Quality submodule).

Implementation notes

This implementation supports the following optional features of the format:

line breaks and/or other whitespace characters in any part of the sequence and/or qualities (only when reading!)
writing the ID to the +-line also (line is always ignored when reading)

Member Data Documentation

◆ file_extensions

std::vector<std::string> seqan3::format_fastq::file_extensions

inlinestatic

Initial value:

{
        { "fastq" },
        { "fq"    }
    }

The valid file extensions for this format; note that you can modify this value.

The documentation for this struct was generated from the following file:

seqan3/io/sequence_file/format_fastq.hpp