42template <
typename format_type>
49 template <
typename... ts>
52 format_type::write_alignment_record(std::forward<ts>(args)...);
56 template <
typename stream_t,
typename header_type>
59 format_type::write_header(stream, options, header);
81concept sam_file_output_format =
requires (detail::sam_file_output_format_exposer<t> & v,
83 sam_file_output_options & options,
84 sam_file_header<> & header,
95 sam_tag_dictionary & tag_dict,
101 v.write_alignment_record(stream,
117 } -> std::same_as<void>;
122#if SEQAN3_DOXYGEN_ONLY(1) 0
207template <
typename... ts>
Provides aliases for qualified.
Provides the seqan3::cigar alphabet.
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
constexpr bool is_type_list_of_sam_file_output_formats_v
Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqa...
Definition sam_file/output_format_concept.hpp:200
@ 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.
@ 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 internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Provides seqan3::phred42 quality scores.
Provides seqan3::sam_file_output_options.
Provides helper data structures for the seqan3::sam_file_output.
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
The options type defines various option members that influence the behavior of all or some formats.
Definition sam_file/output_options.hpp:23
Type that contains multiple types.
Definition type_list.hpp:26
Provides seqan3::type_list.