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seqan3::sequence_file_input_format< t > Interface Template Reference
IO » Sequence File

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 >:
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## 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.

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

- sequence_file/input_format_concept.hpp

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