SeqAn3  3.1.0
The Modern C++ library for sequence analysis.
input_format_concept.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2021, 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 
30 
31 namespace seqan3::detail
32 {
33 
44 template <typename format_type>
45 struct sam_file_input_format_exposer : public format_type
46 {
47 public:
48  // Can't use `using format_type::read_alignment_record` as it produces a hard failure in the format concept check
49  // for types that do not model the format concept, i.e. don't offer the proper read_alignment_record interface.
51  template <typename ...ts>
52  void read_alignment_record(ts && ...args)
53  {
54  format_type::read_alignment_record(std::forward<ts>(args)...);
55  }
56 };
57 
58 } // namespace seqan3::detail
59 
60 namespace seqan3
61 {
62 
76 template <typename t>
77 SEQAN3_CONCEPT sam_file_input_format =
78  requires (detail::sam_file_input_format_exposer<t> & v,
79  std::ifstream & stream,
80  sam_file_input_options<dna5> & options,
81  std::vector<dna5_vector> & ref_sequences,
82  sam_file_header<> & header,
83  dna5_vector & seq,
84  std::vector<phred42> & qual,
85  std::string & id,
86  int32_t & offset,
87  dna5_vector & ref_seq,
88  std::optional<int32_t> & ref_id,
89  std::optional<int32_t> & ref_offset,
90  std::pair<std::vector<gapped<dna4>>, std::vector<gapped<dna4>>> & align,
91  std::vector<cigar> & cigar,
92  sam_flag & flag,
93  uint8_t & mapq,
95  sam_tag_dictionary & tag_dict,
96  double & e_value,
97  double & bit_score)
98 {
99  t::file_extensions;
100  // std::same_as<decltype(t::file_extensions), std::vector<std::string>>;
101 
102  { v.read_alignment_record(stream,
103  options,
104  ref_sequences,
105  header,
106  seq,
107  qual,
108  id,
109  offset,
110  ref_seq,
111  ref_id,
112  ref_offset,
113  align,
114  cigar,
115  flag,
116  mapq,
117  mate,
118  tag_dict,
119  e_value,
120  bit_score)};
121 
122  { v.read_alignment_record(stream,
123  options,
124  std::ignore,
125  header,
126  std::ignore,
127  std::ignore,
128  std::ignore,
129  std::ignore,
130  std::ignore,
131  std::ignore,
132  std::ignore,
133  std::ignore,
134  std::ignore,
135  std::ignore,
136  std::ignore,
137  std::ignore,
138  std::ignore,
139  std::ignore,
140  std::ignore)};
141 };
143 
220 
221 } // namespace seqan3
222 
223 namespace seqan3::detail
224 {
225 
231 template <typename t>
232 constexpr bool is_type_list_of_sam_file_input_formats_v = false;
233 
239 template <typename ...ts>
240 constexpr bool is_type_list_of_sam_file_input_formats_v<type_list<ts...>> = (sam_file_input_format<ts> && ...);
241 
247 template <typename t>
248 SEQAN3_CONCEPT type_list_of_sam_file_input_formats = is_type_list_of_sam_file_input_formats_v<t>;
249 
250 } // namespace seqan3::detail
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.
Provides seqan3::gapped.
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:76
Provides the seqan3::sam_file_header class.
The generic concept for alignment file input formats.
void read_alignment_record(stream_type &stream, sam_file_input_options< seq_legal_alph_type > const &options, ref_seqs_type &ref_seqs, header_type &header, seq_type &seq, qual_type &qual, id_type &id, offset_type &offset, ref_seq_type &ref_seq, ref_id_type &ref_id, ref_offset_type &ref_offset, align_type &align, cigar_type &cigar_vector, flag_type &flag, mapq_type &mapq, mate_type &mate, tag_dict_type &tag_dict, e_value_type &e_value, bit_score_type &bit_score)
Read from the specified stream and back-insert into the given field buffers.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::phred42 quality scores.
Provides seqan3::sam_file_input_options.
Provides helper data structures for the seqan3::sam_file_output.
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
Provides seqan3::type_list.