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seqan3::sam_file_output_format< t > Interface Template Reference
IO » SAM File

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

`#include <seqan3/io/sam_file/output_format_concept.hpp>`

## Related Symbols

(Note that these are not member symbols.)
Requirements for seqan3::sam_file_output_format
You can expect these members on all types that implement seqan3::sam_file_output_format.

void

write_alignment_record (stream_type &stream, sam_file_output_options const &options, sam_file_header<> &header, seq_type &&seq, qual_type &&qual, id_type &&id, ref_seq_type &&ref_seq, ref_id_type &&ref_id, ref_offset_type &&ref_offset, std::vector< cigar > &cigar_vector, flag_type &&flag, mapq_type &&mapq, mate_type &&mate, tag_dict_type &&tag_dict, e_value_type &&e_value, bit_score_type &&bit_score)

| Write the given fields to the specified stream.
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::sam_file_output_format< t >

The generic concept for alignment 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 model this concept are shown as "implementing this interface".

## Friends And Related Symbol Documentation

## write_alignment_record()

template<typename t>

void write_alignment_record | ( | stream_type & | stream,
|  | sam_file_output_options const & | options,
|  | sam_file_header<> & | header,
|  | seq_type && | seq,
|  | qual_type && | qual,
|  | id_type && | id,
|  | ref_seq_type && | ref_seq,
|  | ref_id_type && | ref_id,
|  | ref_offset_type && | ref_offset,
|  | std::vector< cigar > & | cigar_vector,
|  | flag_type && | flag,
|  | mapq_type && | mapq,
|  | mate_type && | mate,
|  | tag_dict_type && | tag_dict,
|  | e_value_type && | e_value,
|  | bit_score_type && | bit_score )

related

Write the given fields to the specified stream.

Template Parameters

  stream_type | Output stream, must model seqan3::output_stream_over with char.
  seq_type | Type of the seqan3
  id_type | Type of the seqan3
  ref_seq_type | Type of the seqan3
  ref_id_type | Type of the seqan3
  ref_offset_type | Type of the seqan3
  flag_type | Type of the seqan3
  mapq_type | Type of the seqan3
  qual_type | Type of the seqan3
  mate_type | Type of the seqan3
  tag_dict_type | Type of the seqan3
  e_value_type | Type of the seqan3
  bit_score_type | Type of the seqan3

Parameters

  [in,out] | stream | The output stream to write into.
  [in] | options | File specific options passed to the format.
  [in] | header | A pointer to the header object of the file.
  [in] | seq | The data for seqan3::field::seq, i.e. the query sequence.
  [in] | qual | The data for seqan3::field::qual, e.g. the query quality sequence.
  [in] | id | The data for seqan3::field::id, e.g. the read id.
  [in] | ref_seq | The data for seqan3::field::ref_offset, i.e. the reference sequence.
  [in] | ref_id | The data for seqan3::field::ref_id, e.g. the reference id..
  [in] | ref_offset | The data for seqan3::field::ref_offset, i.e. the start position of the alignment in `ref_seq`.
  [in] | cigar_vector | The data for seqan3::field::cigar, e.g. representing the alignment between query and ref.
  [in] | flag | The data for seqan3::field::flag, e.g. the SAM mapping flag value.
  [in] | mapq | The data for seqan3::field::mapq, e.g. the mapping quality value.
  [in] | mate | The data for seqan3::field::mate, e.g. the mate information of paired reads.
  [in] | tag_dict | The data for seqan3::field::tags, e.g. the optional SAM field tag dictionary.
  [in] | e_value | The data for seqan3::field::e_value, e.g. the e-value of the alignment (BLAST).
  [in] | bit_score | The data for seqan3::field::, e.g. the bit score of the alignment (BLAST).

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

- sam_file/output_format_concept.hpp

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