SeqAn3  3.0.1
The Modern C++ library for sequence analysis.
output_format_concept.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
13 #pragma once
14 
15 #include <fstream>
16 #include <string>
17 #include <vector>
18 
29 
30 namespace seqan3::detail
31 {
32 
43 template <typename format_type>
44 struct alignment_file_output_format_exposer : public format_type
45 {
46 public:
47  // Can't use `using format_type::write_alignment_record` as it produces a hard failure in the format concept check
48  // for types that do not model the format concept, i.e. don't offer the proper write_alignment_record interface.
50  template <typename ...ts>
51  void write_alignment_record(ts && ...args)
52  {
53  format_type::write_alignment_record(std::forward<ts>(args)...);
54  }
55 };
56 
57 } // namespace seqan3::detail
58 
59 namespace seqan3
60 {
61 
73 template <typename t>
75 SEQAN3_CONCEPT alignment_file_output_format =
76  requires (detail::alignment_file_output_format_exposer<t> & v,
77  std::ofstream & stream,
78  alignment_file_output_options & options,
79  alignment_file_header<> & header,
80  dna5_vector & seq,
82  std::string & id,
83  int32_t & offset,
84  dna5_vector & ref_seq,
87  std::pair<std::vector<gapped<dna4>>, std::vector<gapped<dna4>>> & align,
89  sam_flag & flag,
90  uint8_t & mapq,
92  sam_tag_dictionary & tag_dict,
93  double & e_value,
94  double & bit_score)
95 {
96  t::file_extensions;
97 
98  { v.write_alignment_record(stream,
99  options,
100  header,
101  seq,
102  qual,
103  id,
104  offset,
105  ref_seq,
106  ref_id,
107  ref_offset,
108  align,
109  cigar,
110  flag,
111  mapq,
112  mate,
113  tag_dict,
114  e_value,
115  bit_score
116  ) } -> void;
117 };
119 
185 
187 } // namespace seqan3
188 
189 namespace seqan3::detail
190 {
191 
197 template <typename t>
198 constexpr bool is_type_list_of_alignment_file_output_formats_v = false;
199 
205 template <typename ...ts>
206 constexpr bool is_type_list_of_alignment_file_output_formats_v<type_list<ts...>>
207  = (alignment_file_output_format<ts> && ...);
208 
214 template <typename t>
215 SEQAN3_CONCEPT type_list_of_alignment_file_output_formats = is_type_list_of_alignment_file_output_formats_v<t>;
216 } // namespace seqan3::detail
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.
Provides seqan3::alignment_file_output_options.
The qualities, usually in phred-score notation.
Provides seqan3::type_list.
Provides the seqan3::cigar alphabet.
Provides the seqan3::alignment_file_header class.
Provides seqan3::gapped.
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 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.