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

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

Related Functions
(Note that these are not member functions.)
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, offset_type &&offset, ref_seq_type &&ref_seq, ref_id_type &&ref_id, ref_offset_type &&ref_offset, align_type &&align, 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. More...

static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.

Detailed Description

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 Function Documentation

◆ write_alignment_record()

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,
		offset_type &&	offset,
		ref_seq_type &&	ref_seq,
		ref_id_type &&	ref_id,
		ref_offset_type &&	ref_offset,
		align_type &&	align,
		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
	)

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
offset_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
align_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]	offset	The data for seqan3::field::offset, i.e. the start position of the alignment in `seq`.
[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]	align	The data for seqan3::field::align, e.g. the alignment between query and ref.
[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:

seqan3/io/sam_file/output_format_concept.hpp

Related Functions

Detailed Description

Friends And Related Function Documentation

◆ write_alignment_record()