29namespace seqan3::detail
42template <
typename format_type>
43struct sam_file_input_format_exposer :
public format_type
49 template <
typename... ts>
50 void read_alignment_record(ts &&... args)
52 format_type::read_alignment_record(std::forward<ts>(args)...);
75concept sam_file_input_format =
requires (detail::sam_file_input_format_exposer<t> & v,
77 sam_file_input_options<dna5> & options,
79 sam_file_header<> & header,
91 sam_tag_dictionary & tag_dict,
98 v.read_alignment_record(stream,
119 v.read_alignment_record(stream,
143#if SEQAN3_DOXYGEN_ONLY(1) 0
225namespace seqan3::detail
234constexpr bool is_type_list_of_sam_file_input_formats_v =
false;
241template <
typename... ts>
242constexpr bool is_type_list_of_sam_file_input_formats_v<type_list<ts...>> = (sam_file_input_format<ts> && ...);
250concept type_list_of_sam_file_input_formats = is_type_list_of_sam_file_input_formats_v<t>;
Provides aliases for qualified.
Provides the seqan3::cigar alphabet.
Provides seqan3::dna4, container aliases and string literals.
Provides seqan3::dna5, container aliases and string literals.
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition sam_flag.hpp:73
@ flag
The alignment flag (bit information), uint16_t value.
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
@ ref_seq
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
@ mapq
The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.
@ bit_score
The bit score (statistical significance indicator), unsigned value.
@ mate
The mate pair information given as a std::tuple of reference name, offset and template length.
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
@ id
The identifier, usually a string.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
@ qual
The qualities, usually in Phred score notation.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Provides seqan3::phred42 quality scores.
Provides helper data structures for the seqan3::sam_file_output.
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
Provides seqan3::type_list.