SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::sequence_file_input_format Interface 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:

Related Functions

(Note that these are not member functions.)

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, seq_type &sequence, id_type &id, qual_type &qualities)
 Read from the specified stream and back-insert into the given field buffers. More...
 
static inline std::vector< std::stringfile_extensions
 The format type is required to provide a vector of all supported file extensions.
 

Detailed Description

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".

Friends And Related Function Documentation

◆ read_sequence_record()

void read_sequence_record ( stream_type &  stream,
seqan3::sequence_file_input_options const &  options,
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_typeInput stream, must satisfy seqan3::input_stream_over with char.
seq_typeType of the seqan3::field::seq input; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_typeType of the seqan3::field::id input; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_typeType of the seqan3::field::qual input; must satisfy std::ranges::output_range over a seqan3::writable_quality_alphabet.
Parameters
[in,out]streamThe input stream to read from.
[in]optionsFile specific options passed to the format.
[out]sequenceThe buffer for seqan3::field::seq input, i.e. the "sequence".
[out]idThe buffer for seqan3::field::id input, e.g. the header line in FastA.
[out]qualitiesThe buffer for seqan3::field::qual input.

Additional requirements


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