seqan3::SequenceFileOutputFormat Interface Reference

The generic concept for sequence file out formats. More...

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

Inheritance diagram for seqan3::SequenceFileOutputFormat:

Related Functions
(Note that these are not member functions.)
Requirements for seqan3::SequenceFileOutputFormat
You can expect these members on all types that implement seqan3::SequenceFileOutputFormat.
void	write (stream_type &stream, seqan3::sequence_file_output_options const &options, seq_type &&sequence, id_type &&id, qual_type &&qualities)
	Write the given fields to the specified stream. More...
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.

Detailed Description

The generic concept for sequence file out formats.

The details of this concept are only relevant to developers who wish to implement their own format. The requirements for this concept are given as related functions and type traits. Types that satisfy this concept are shown as "implementing this interface".

Friends And Related Function Documentation

write()

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

related

Write the given fields to the specified stream.

Template Parameters

stream_type	Output stream, must satisfy seqan3::OStream with char.
seq_type	Type of the seqan3::field::SEQ output; must satisfy std::ranges::OutputRange over a seqan3::Alphabet.
id_type	Type of the seqan3::field::ID output; must satisfy std::ranges::OutputRange over a seqan3::Alphabet.
qual_type	Type of the seqan3::field::QUAL output; must satisfy std::ranges::OutputRange over a seqan3::QualityAlphabet.

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]
• The format does not handle seqan3::field::SEQ_QUAL, instead seqan3::sequence_file_output splits it into two views and passes it to the format as if they were separate.

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

• seqan3/io/sequence_file/output_format_concept.hpp