44 template <
typename format_type>
45 struct alignment_file_input_format_exposer :
public format_type
51 template <
typename ...ts>
52 void read_alignment_record(ts && ...args)
54 format_type::read_alignment_record(std::forward<ts>(args)...);
75 SEQAN3_CONCEPT alignment_file_input_format =
76 requires (detail::alignment_file_input_format_exposer<t> & v,
78 alignment_file_input_options<dna5> & options,
80 alignment_file_header<> & header,
93 sam_tag_dictionary & tag_dict,
100 { v.read_alignment_record(stream,
120 { v.read_alignment_record(stream,
229 template <
typename t>
230 constexpr
bool is_type_list_of_alignment_file_input_formats_v =
false;
237 template <
typename ...ts>
238 constexpr
bool is_type_list_of_alignment_file_input_formats_v<
type_list<ts...>> =
239 (alignment_file_input_format<ts> && ...);
246 template <
typename t>
247 SEQAN3_CONCEPT type_list_of_alignment_file_input_formats = is_type_list_of_alignment_file_input_formats_v<t>;
meta::list< types... > type_list
Type that contains multiple types, an alias for meta::list.
Definition: type_list.hpp:31
Sequence (REF_SEQ) relative start position (0-based), unsigned value.
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
The mate pair information given as a std::tuple of reference name, offset and template length...
The main SeqAn3 namespace.
The "sequence", usually a range of nucleotides or amino acids.
Provides seqan3::dna5, container aliases and string literals.
The alignment flag (bit information), uint16_t value.
The qualities, usually in phred-score notation.
Provides seqan3::type_list.
Provides the seqan3::cigar alphabet.
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format...
Definition: aligned_sequence_concept.hpp:36
Sequence (SEQ) relative start position (0-based), unsigned value.
Provides seqan3::phred42 quality scores.
Provides helper data structures for the seqan3::alignment_file_output.
The bit score (statistical significance indicator), unsigned value.
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).The SAM flag are bitwise flags, which means that each value corresponds to a specific bit that is set and that they can be combined and tested using binary operations. See this tutorial for an introduction on bitwise operations on enum flags.
Definition: misc.hpp:70
Provides seqan3::dna4, container aliases and string literals.
Provides aliases for qualified.
The mapping quality of the SEQ alignment, usually a ohred-scaled score.
The identifier of the (reference) sequence that SEQ was aligned to.