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

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

Related Symbols
(Note that these are not member symbols.)
Requirements for seqan3::sam_file_input_format
You can expect these members on all types that implement seqan3::sam_file_input_format.
void	read_alignment_record (stream_type &stream, sam_file_input_options< seq_legal_alph_type > const &options, ref_seqs_type &ref_seqs, header_type &header, stream_pos_type &position_buffer, seq_type &seq, qual_type &qual, id_type &id, ref_seq_type &ref_seq, ref_id_type &ref_id, ref_offset_type &ref_offset, cigar_type &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)
	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::sam_file_input_format< t >

The generic concept for alignment file input 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 SAM File

Friends And Related Symbol Documentation

◆ read_alignment_record()

template<typename t >

void read_alignment_record	(	stream_type &	stream,
		sam_file_input_options< seq_legal_alph_type > const &	options,
		ref_seqs_type &	ref_seqs,
		header_type &	header,
		stream_pos_type &	position_buffer,
		seq_type &	seq,
		qual_type &	qual,
		id_type &	id,
		ref_seq_type &	ref_seq,
		ref_id_type &	ref_id,
		ref_offset_type &	ref_offset,
		cigar_type &	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	The input stream type; Must be derived from std::ostream.
stream_pos_type	Type of the position buffer, aka, the std::streampos of the current record.
ref_seqs_type	e.g. std::deque<ref_sequence_type> or decltype(std::ignore).
seq_type	Type of the seqan3::field::seq input (see seqan3::sam_file_input_traits).
qual_type	Type of the seqan3::field::qual input (see seqan3::sam_file_input_traits).
id_type	Type of the seqan3::field::id input (see seqan3::sam_file_input_traits).
ref_seq_type	Type of the seqan3::field::ref_seq input (see seqan3::sam_file_input_traits).
ref_id_type	Type of the seqan3::field::ref_id input (see seqan3::sam_file_input_traits).
ref_offset_type	Type of the seqan3::field::ref_offset input (see seqan3::sam_file_input_traits).
cigar_type	Type of the seqan3::field::cigar input (a std::vector<cigar> or std::ignore).
flag_type	Type of the seqan3::field::flag input (see seqan3::sam_file_input_traits).
mapq_type	Type of the seqan3::field::mapq input (see seqan3::sam_file_input_traits).
mate_type	std::tuple<ref_id_type, ref_offset_type, int32_t> or decltype(std::ignore).
tag_dict_type	seqan3::sam_tag_dictionary or decltype(std::ignore).
e_value_type	Type of the seqan3::field::evalue input (see seqan3::sam_file_input_traits).
bit_score_type	Type of the seqan3::field::bit_score input (see seqan3::sam_file_input_traits).

Parameters

[in,out]	stream	The input stream to read from.
[in,out]	position_buffer	The buffer to store the current record's position.
[in]	options	File specific options passed to the format.
[out]	ref_seqs	The reference sequences to the corresponding alignments.
[out]	header	A pointer to the seqan3::sam_file_header object.
[out]	seq	The buffer for seqan3::field::seq input.
[out]	qual	The buffer for seqan3::field::qual input.
[out]	id	The buffer for seqan3::field::id input.
[out]	ref_seq	The buffer for seqan3::field::ref_seq input.
[out]	ref_id	The buffer for seqan3::field::ref_id input.
[out]	ref_offset	The buffer for seqan3::field::ref_offset input.
[out]	cigar_vector	The buffer for seqan3::field::cigar input.
[out]	flag	The buffer for seqan3::field::flag input.
[out]	mapq	The buffer for seqan3::field::mapq input.
[out]	mate	The buffer for seqan3::field::mate input.
[out]	tag_dict	The buffer for seqan3::field::tags input.
[out]	e_value	The buffer for seqan3::field::evalue input.
[out]	bit_score	The buffer for seqan3::field::bit_score input.

Additional requirements

The function must also accept std::ignore as parameter for any of the fields, except stream, options and header. [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:

sam_file/input_format_concept.hpp

Related Symbols

Detailed Description

Friends And Related Symbol Documentation

◆ read_alignment_record()

Additional requirements