SeqAn3 3.3.0-rc.1
The Modern C++ library for sequence analysis.
sam_file/input_format_concept.hpp
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1// -----------------------------------------------------------------------------------------------------
2// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3// Copyright (c) 2016-2022, 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 <optional>
17#include <string>
18#include <vector>
19
20#include <seqan3/alphabet/cigar/cigar.hpp>
21#include <seqan3/alphabet/gap/gapped.hpp>
22#include <seqan3/alphabet/nucleotide/dna4.hpp>
23#include <seqan3/alphabet/nucleotide/dna5.hpp>
24#include <seqan3/alphabet/quality/aliases.hpp>
25#include <seqan3/alphabet/quality/phred42.hpp>
26#include <seqan3/io/sam_file/header.hpp>
27#include <seqan3/io/sam_file/input_options.hpp>
28#include <seqan3/io/sam_file/sam_flag.hpp>
29#include <seqan3/io/sam_file/sam_tag_dictionary.hpp>
30#include <seqan3/utility/type_list/type_list.hpp>
31
32namespace seqan3::detail
33{
34
45template <typename format_type>
46struct sam_file_input_format_exposer : public format_type
47{
48public:
49 // Can't use `using format_type::read_alignment_record` as it produces a hard failure in the format concept check
50 // for types that do not model the format concept, i.e. don't offer the proper read_alignment_record interface.
52 template <typename... ts>
53 void read_alignment_record(ts &&... args)
54 {
55 format_type::read_alignment_record(std::forward<ts>(args)...);
56 }
57};
58
59} // namespace seqan3::detail
60
61namespace seqan3
62{
63
77template <typename t>
78concept sam_file_input_format = 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 std::streampos & position_buffer,
84 dna5_vector & seq,
85 std::vector<phred42> & qual,
86 std::string & id,
87 int32_t & offset,
88 dna5_vector & ref_seq,
89 std::optional<int32_t> & ref_id,
90 std::optional<int32_t> & ref_offset,
91 std::vector<cigar> & cigar,
92 sam_flag & flag,
93 uint8_t & mapq,
94 std::tuple<std::optional<int32_t>, std::optional<int32_t>, int32_t> & mate,
95 sam_tag_dictionary & tag_dict,
96 double & e_value,
97 double & bit_score) {
98 t::file_extensions;
99 // std::same_as<decltype(t::file_extensions), std::vector<std::string>>;
100
101 {
102 v.read_alignment_record(stream,
103 options,
104 ref_sequences,
105 header,
106 position_buffer,
107 seq,
108 qual,
109 id,
110 offset,
111 ref_seq,
112 ref_id,
113 ref_offset,
114 cigar,
115 flag,
116 mapq,
117 mate,
118 tag_dict,
119 e_value,
120 bit_score)
121 };
122
123 {
124 v.read_alignment_record(stream,
125 options,
126 std::ignore,
127 header,
128 position_buffer,
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 std::ignore,
142 std::ignore)
143 };
144 };
146
147// Workaround for https://github.com/doxygen/doxygen/issues/9379
148#if SEQAN3_DOXYGEN_ONLY(1) 0
149template <typename t>
150class sam_file_input_format
151{};
152#endif
153
230
231} // namespace seqan3
232
233namespace seqan3::detail
234{
235
241template <typename t>
242constexpr bool is_type_list_of_sam_file_input_formats_v = false;
243
249template <typename... ts>
250constexpr bool is_type_list_of_sam_file_input_formats_v<type_list<ts...>> = (sam_file_input_format<ts> && ...);
251
257template <typename t>
258concept type_list_of_sam_file_input_formats = is_type_list_of_sam_file_input_formats_v<t>;
259
260} // namespace seqan3::detail
aliases.hpp
Provides aliases for qualified.
cigar.hpp
Provides the seqan3::cigar alphabet.
seqan3::sam_file_input_format
The generic concept for alignment file input formats.
Definition: sam_file/input_format_concept.hpp:151
dna4.hpp
Provides seqan3::dna4, container aliases and string literals.
dna5.hpp
Provides seqan3::dna5, container aliases and string literals.
gapped.hpp
Provides seqan3::gapped.
seqan3::sam_flag
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:76
seqan3::field::flag
@ flag
The alignment flag (bit information), uint16_t value.
seqan3::field::ref_offset
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
seqan3::field::ref_seq
@ ref_seq
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
seqan3::field::cigar
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
seqan3::field::mapq
@ mapq
The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.
seqan3::field::bit_score
@ bit_score
The bit score (statistical significance indicator), unsigned value.
seqan3::field::offset
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
seqan3::field::mate
@ mate
The mate pair information given as a std::tuple of reference name, offset and template length.
seqan3::field::ref_id
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
seqan3::field::id
@ id
The identifier, usually a string.
seqan3::field::seq
@ seq
The "sequence", usually a range of nucleotides or amino acids.
seqan3::field::qual
@ qual
The qualities, usually in Phred score notation.
header.hpp
Provides the seqan3::sam_file_header class.
seqan3
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
phred42.hpp
Provides seqan3::phred42 quality scores.
input_options.hpp
Provides seqan3::sam_file_input_options.
sam_flag.hpp
Provides helper data structures for the seqan3::sam_file_output.
sam_tag_dictionary.hpp
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
type_list.hpp
Provides seqan3::type_list.