seqan3::sequence_file_input_format< t > Interface Template Reference

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

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

Inheritance diagram for seqan3::sequence_file_input_format< t >:

Related Symbols
(Note that these are not member symbols.)
Requirements for seqan3::sequence_file_input_format
You can expect these members on all types that implement seqan3::sequence_file_input_format.
void	read_sequence_record (stream_type &stream, seqan3::sequence_file_input_options 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.
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.

Detailed Description

template<typename t>
interface seqan3::sequence_file_input_format< t >

The generic concept for sequence file in 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".

Remarks

For a complete overview, take a look at Sequence File

Friends And Related Symbol Documentation

read_sequence_record()

template<typename t >

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

related

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.

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

• sequence_file/input_format_concept.hpp