seqan3::format_fastq Class Reference

The FASTQ format. More...

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

Inheritance diagram for seqan3::format_fastq:

Public Member Functions
Constructors, destructor and assignment
	format_fastq () noexcept=default
	Defaulted.
	format_fastq (format_fastq const &) noexcept=default
	Defaulted.
format_fastq &	operator= (format_fastq const &) noexcept=default
	Defaulted.
	format_fastq (format_fastq &&) noexcept=default
	Defaulted.
format_fastq &	operator= (format_fastq &&) noexcept=default
	Defaulted.
	~format_fastq () noexcept=default
	Defaulted.

Static Public Attributes
static std::vector< std::string >	file_extensions {{"fastq"}, {"fq"}}
	The valid file extensions for this format; note that you can modify this value.

Protected Member Functions
template<typename stream_type , typename seq_legal_alph_type , typename stream_pos_type , typename seq_type , typename id_type , typename qual_type >
void	read_sequence_record (stream_type &stream, sequence_file_input_options< seq_legal_alph_type > const &options, stream_pos_type &position_buffer, seq_type &sequence, id_type &id, qual_type &qualities)
	Read from the specified stream and back-insert into the given field buffers.
template<typename stream_type , typename seq_type , typename id_type , typename qual_type >
void	write_sequence_record (stream_type &stream, sequence_file_output_options const &options, seq_type &&sequence, id_type &&id, qual_type &&qualities)
	Write the given fields to the specified stream.

Detailed Description

The FASTQ format.

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_specialisation

The FASTQ format provides the fields seqan3::field::seq, seqan3::field::id and seqan3::field::qual. All three fields 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::sequence_file_input_traits 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)

Remarks

For a complete overview, take a look at Sequence File

Member Function Documentation

read_sequence_record()

template<typename stream_type , typename seq_legal_alph_type , typename stream_pos_type , typename seq_type , typename id_type , typename qual_type >

void seqan3::format_fastq::read_sequence_record ( stream_type &  stream, sequence_file_input_options< seq_legal_alph_type > const &  options, stream_pos_type &  position_buffer, seq_type &  sequence, id_type &  id, qual_type &  qualities  )

inlineprotected

Read from the specified stream and back-insert into the given field buffers.

Template Parameters

stream_type	Input stream, must satisfy seqan3::input_stream_over with char.
stream_pos_type	Buffer for storing the current record's file position.
seq_type	Type of the seqan3::field::seq input; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id input; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_type	Type of the seqan3::field::qual input; must satisfy std::ranges::output_range over a seqan3::writable_quality_alphabet.

Parameters

[in,out]	stream	The input stream to read from.
[in,out]	position_buffer	The buffer to store the current record's file position.
[in]	options	File specific options passed to the format.
[out]	sequence	The buffer for seqan3::field::seq input, i.e. the "sequence".
[out]	id	The buffer for seqan3::field::id input, e.g. the header line in FASTA .
[out]	qualities	The buffer for seqan3::field::qual input.

Additional requirements

• The function must also accept std::ignore as parameter for any of the fields. [This is enforced by the concept checker!]
• In this case the data read for that field shall be discarded by the format.

write_sequence_record()

template<typename stream_type , typename seq_type , typename id_type , typename qual_type >

void seqan3::format_fastq::write_sequence_record ( stream_type &  stream, sequence_file_output_options const &  options, seq_type &&  sequence, id_type &&  id, qual_type &&  qualities  )

inlineprotected

Write the given fields to the specified stream.

Template Parameters

stream_type	Output stream, must satisfy seqan3::output_stream_over with char.
seq_type	Type of the seqan3::field::seq output; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id output; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_type	Type of the seqan3::field::qual output; must satisfy std::ranges::output_range over a seqan3::quality_alphabet.

Parameters

[in,out]	stream	The output stream to write into.
[in]	options	File specific options passed to the format.
[in]	sequence	The data for seqan3::field::seq, i.e. the "sequence".
[in]	id	The data for seqan3::field::id, e.g. the header line in FASTA.
[in]	qualities	The data for seqan3::field::qual.

Additional requirements

• The format must also accept std::ignore as parameter for any of the fields, however it shall throw an exception if one of the fields required for writing the format is marked as such. [this shall be checked inside the function]

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

• format_fastq.hpp