SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::sam_file_output_format< t > Interface Template Reference

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::stringfile_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 

Write the given fields to the specified stream.

Template Parameters
stream_typeOutput stream, must model seqan3::output_stream_over with char.
seq_typeType of the seqan3
id_typeType of the seqan3
ref_seq_typeType of the seqan3
ref_id_typeType of the seqan3
ref_offset_typeType of the seqan3
flag_typeType of the seqan3
mapq_typeType of the seqan3
qual_typeType of the seqan3
mate_typeType of the seqan3
tag_dict_typeType of the seqan3
e_value_typeType of the seqan3
bit_score_typeType of the seqan3
[in,out]streamThe output stream to write into.
[in]optionsFile specific options passed to the format.
[in]headerA pointer to the header object of the file.
[in]seqThe data for seqan3::field::seq, i.e. the query sequence.
[in]qualThe data for seqan3::field::qual, e.g. the query quality sequence.
[in]idThe data for seqan3::field::id, e.g. the read id.
[in]ref_seqThe data for seqan3::field::ref_offset, i.e. the reference sequence.
[in]ref_idThe data for seqan3::field::ref_id, e.g. the reference id..
[in]ref_offsetThe data for seqan3::field::ref_offset, i.e. the start position of the alignment in ref_seq.
[in]cigar_vectorThe data for seqan3::field::cigar, e.g. representing the alignment between query and ref.
[in]flagThe data for seqan3::field::flag, e.g. the SAM mapping flag value.
[in]mapqThe data for seqan3::field::mapq, e.g. the mapping quality value.
[in]mateThe data for seqan3::field::mate, e.g. the mate information of paired reads.
[in]tag_dictThe data for seqan3::field::tags, e.g. the optional SAM field tag dictionary.
[in]e_valueThe data for seqan3::field::e_value, e.g. the e-value of the alignment (BLAST).
[in]bit_scoreThe data for seqan3::field::, e.g. the bit score of the alignment (BLAST).

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