30 namespace seqan3::detail
43 template <
typename format_type>
44 struct sam_file_output_format_exposer :
public format_type
50 template <
typename ...ts>
51 void write_alignment_record(ts && ...args)
53 format_type::write_alignment_record(std::forward<ts>(args)...);
76 requires (detail::sam_file_output_format_exposer<t> & v,
77 std::ofstream & stream,
78 sam_file_output_options & options,
79 sam_file_header<> & header,
81 std::vector<phred42> & qual,
84 dna5_vector & ref_seq,
85 std::optional<int32_t> & ref_id,
86 std::optional<int32_t> & ref_offset,
87 std::pair<std::vector<gapped<dna4>>, std::vector<gapped<dna4>>> & align,
88 std::vector<cigar> & cigar,
91 std::tuple<std::optional<int32_t>, std::optional<int32_t>, int32_t> & mate,
92 sam_tag_dictionary & tag_dict,
189 namespace seqan3::detail
197 template <
typename t>
198 constexpr
bool is_type_list_of_sam_file_output_formats_v =
false;
205 template <
typename ...ts>
213 template <
typename t>
214 SEQAN3_CONCEPT type_list_of_sam_file_output_formats = is_type_list_of_sam_file_output_formats_v<t>;
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
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::phred42 quality scores.
Provides seqan3::sam_file_output_options.
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
Provides helper data structures for the seqan3::sam_file_output.
Provides seqan3::type_list.