SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
record.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 <seqan3/io/record.hpp>
16 
17 namespace seqan3
18 {
25 template <typename field_types, typename field_ids>
26 class sam_record : public record<field_types, field_ids>
27 {
29  using base_t = record<field_types, field_ids>;
30 
32  using tuple_base_t = typename base_t::base_type;
33 
35  template <field f>
36  using field_constant = typename base_t::template field_constant<f>;
37 
38  using base_t::get_impl;
39 public:
43  sam_record() = default;
44  sam_record(sam_record const &) = default;
45  sam_record & operator=(sam_record const &) = default;
46  sam_record(sam_record &&) = default;
47  sam_record & operator=(sam_record &&) = default;
48  ~sam_record() = default;
49 
51  using base_t::base_t;
53 
57  decltype(auto) id() &&
58  {
59  return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t &&>(*this));
60  }
62  decltype(auto) id() const &&
63  {
64  return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t const &&>(*this));
65  }
67  decltype(auto) id() &
68  {
69  return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t &>(*this));
70  }
72  decltype(auto) id() const &
73  {
74  return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t const &>(*this));
75  }
76 
80  decltype(auto) sequence() &&
81  {
82  return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t &&>(*this));
83  }
85  decltype(auto) sequence() const &&
86  {
87  return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t const &&>(*this));
88  }
90  decltype(auto) sequence() &
91  {
92  return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t &>(*this));
93  }
95  decltype(auto) sequence() const &
96  {
97  return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t const &>(*this));
98  }
99 
103  decltype(auto) base_qualities() &&
104  {
105  return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t &&>(*this));
106  }
108  decltype(auto) base_qualities() const &&
109  {
110  return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t const &&>(*this));
111  }
113  decltype(auto) base_qualities() &
114  {
115  return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t &>(*this));
116  }
118  decltype(auto) base_qualities() const &
119  {
120  return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t const &>(*this));
121  }
122 
132  decltype(auto) sequence_position() &&
133  {
134  return get_impl(field_constant<seqan3::field::offset>{}, static_cast<tuple_base_t &&>(*this));
135  }
137  decltype(auto) sequence_position() const &&
138  {
139  return get_impl(field_constant<seqan3::field::offset>{}, static_cast<tuple_base_t const &&>(*this));
140  }
142  decltype(auto) sequence_position() &
143  {
144  return get_impl(field_constant<seqan3::field::offset>{}, static_cast<tuple_base_t &>(*this));
145  }
147  decltype(auto) sequence_position() const &
148  {
149  return get_impl(field_constant<seqan3::field::offset>{}, static_cast<tuple_base_t const &>(*this));
150  }
151 
155  decltype(auto) alignment() &&
156  {
157  return get_impl(field_constant<seqan3::field::alignment>{}, static_cast<tuple_base_t &&>(*this));
158  }
160  decltype(auto) alignment() const &&
161  {
162  return get_impl(field_constant<seqan3::field::alignment>{}, static_cast<tuple_base_t const &&>(*this));
163  }
165  decltype(auto) alignment() &
166  {
167  return get_impl(field_constant<seqan3::field::alignment>{}, static_cast<tuple_base_t &>(*this));
168  }
170  decltype(auto) alignment() const &
171  {
172  return get_impl(field_constant<seqan3::field::alignment>{}, static_cast<tuple_base_t const &>(*this));
173  }
174 
179  decltype(auto) reference_id() &&
180  {
181  return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t &&>(*this));
182  }
184  decltype(auto) reference_id() const &&
185  {
186  return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t const &&>(*this));
187  }
189  decltype(auto) reference_id() &
190  {
191  return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t &>(*this));
192  }
194  decltype(auto) reference_id() const &
195  {
196  return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t const &>(*this));
197  }
198 
202  decltype(auto) reference_sequence() = delete;
203 
208  decltype(auto) reference_position() &&
209  {
210  return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t &&>(*this));
211  }
213  decltype(auto) reference_position() const &&
214  {
215  return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t const &&>(*this));
216  }
218  decltype(auto) reference_position() &
219  {
220  return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t &>(*this));
221  }
223  decltype(auto) reference_position() const &
224  {
225  return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t const &>(*this));
226  }
227 
233  decltype(auto) header_ptr() &&
234  {
235  return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t &&>(*this));
236  }
238  decltype(auto) header_ptr() const &&
239  {
240  return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t const &&>(*this));
241  }
243  decltype(auto) header_ptr() &
244  {
245  return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t &>(*this));
246  }
248  decltype(auto) header_ptr() const &
249  {
250  return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t const &>(*this));
251  }
252 
256  decltype(auto) flag() &&
257  {
258  return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t &&>(*this));
259  }
261  decltype(auto) flag() const &&
262  {
263  return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t const &&>(*this));
264  }
266  decltype(auto) flag() &
267  {
268  return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t &>(*this));
269  }
271  decltype(auto) flag() const &
272  {
273  return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t const &>(*this));
274  }
275 
283  decltype(auto) mate_reference_id() &&
284  {
285  return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &&>(*this)));
286  }
288  decltype(auto) mate_reference_id() const &&
289  {
290  return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &&>(*this)));
291  }
293  decltype(auto) mate_reference_id() &
294  {
295  return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &>(*this)));
296  }
298  decltype(auto) mate_reference_id() const &
299  {
300  return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &>(*this)));
301  }
302 
306  decltype(auto) mate_position() &&
307  {
308  return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &&>(*this)));
309  }
311  decltype(auto) mate_position() const &&
312  {
313  return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &&>(*this)));
314  }
316  decltype(auto) mate_position() &
317  {
318  return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &>(*this)));
319  }
321  decltype(auto) mate_position() const &
322  {
323  return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &>(*this)));
324  }
325 
329  decltype(auto) template_length() &&
330  {
331  return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &&>(*this)));
332  }
334  decltype(auto) template_length() const &&
335  {
336  return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &&>(*this)));
337  }
339  decltype(auto) template_length() &
340  {
341  return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &>(*this)));
342  }
344  decltype(auto) template_length() const &
345  {
346  return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &>(*this)));
347  }
348 
352  decltype(auto) mapping_quality() &&
353  {
354  return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t &&>(*this));
355  }
357  decltype(auto) mapping_quality() const &&
358  {
359  return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t const &&>(*this));
360  }
362  decltype(auto) mapping_quality() &
363  {
364  return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t &>(*this));
365  }
367  decltype(auto) mapping_quality() const &
368  {
369  return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t const &>(*this));
370  }
371 
375  decltype(auto) cigar_sequence() &&
376  {
377  return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t &&>(*this));
378  }
380  decltype(auto) cigar_sequence() const &&
381  {
382  return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t const &&>(*this));
383  }
385  decltype(auto) cigar_sequence() &
386  {
387  return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t &>(*this));
388  }
390  decltype(auto) cigar_sequence() const &
391  {
392  return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t const &>(*this));
393  }
394 
398  decltype(auto) tags() &&
399  {
400  return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t &&>(*this));
401  }
403  decltype(auto) tags() const &&
404  {
405  return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t const &&>(*this));
406  }
408  decltype(auto) tags() &
409  {
410  return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t &>(*this));
411  }
413  decltype(auto) tags() const &
414  {
415  return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t const &>(*this));
416  }
417 };
418 } // namespace seqan3
419 
420 namespace std
421 {
422 
428 template <typename field_types, typename field_ids>
429 struct tuple_size<seqan3::sam_record<field_types, field_ids>>
430  : tuple_size<typename seqan3::sam_record<field_types, field_ids>::base_type>
431 {};
432 
438 template <size_t elem_no, typename field_types, typename field_ids>
439 struct tuple_element<elem_no, seqan3::sam_record<field_types, field_ids>>
440  : tuple_element<elem_no, typename seqan3::sam_record<field_types, field_ids>::base_type>
441 {};
442 
443 } // namespace std
seqan3::sam_record
The record type of seqan3::alignment_file_input.
Definition: record.hpp:27
seqan3::sam_record::operator=
sam_record & operator=(sam_record &&)=default
Defaulted.
seqan3::sam_record::mate_reference_id
decltype(auto) mate_reference_id() &&
The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)
Definition: record.hpp:283
seqan3::sam_record::cigar_sequence
decltype(auto) cigar_sequence() &&
The cigar vector representing the alignment. (SAM Column ID: CIGAR)
Definition: record.hpp:375
seqan3::sam_record::sequence_position
decltype(auto) sequence_position() &&
Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value....
Definition: record.hpp:132
seqan3::sam_record::header_ptr
decltype(auto) header_ptr() &&
A pointer to the seqan3::sam_file_header object storing header information.
Definition: record.hpp:233
seqan3::sam_record::mapping_quality
decltype(auto) mapping_quality() &&
The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)
Definition: record.hpp:352
seqan3::sam_record::reference_position
decltype(auto) reference_position() &&
(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based),...
Definition: record.hpp:208
seqan3::sam_record::sam_record
sam_record(sam_record const &)=default
Defaulted.
seqan3::sam_record::reference_id
decltype(auto) reference_id() &&
The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to....
Definition: record.hpp:179
seqan3::sam_record::flag
decltype(auto) flag() &&
The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)
Definition: record.hpp:256
seqan3::sam_record::operator=
sam_record & operator=(sam_record const &)=default
Defaulted.
seqan3::sam_record::base_qualities
decltype(auto) base_qualities() &&
The qualities, usually in Phred score notation. (SAM Column ID: QUAL)
Definition: record.hpp:103
seqan3::sam_record::tags
decltype(auto) tags() &&
The optional tags in the SAM format.
Definition: record.hpp:398
seqan3::sam_record::sam_record
sam_record()=default
Defaulted.
seqan3::sam_record::sam_record
sam_record(sam_record &&)=default
Defaulted.
seqan3::sam_record::mate_position
decltype(auto) mate_position() &&
(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)
Definition: record.hpp:306
seqan3::sam_record::reference_sequence
decltype(auto) reference_sequence()=delete
The (reference) "sequence" information, usually a range of nucleotides or amino acids....
seqan3::sam_record::~sam_record
~sam_record()=default
Defaulted.
seqan3::sam_record::alignment
decltype(auto) alignment() &&
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
Definition: record.hpp:155
seqan3::sam_record::template_length
decltype(auto) template_length() &&
The observed template length. (SAM Column ID: TLEN)
Definition: record.hpp:329
seqan3::sam_record::id
decltype(auto) id() &&
The identifier, usually a string. (SAM Column ID: QNAME)
Definition: record.hpp:57
sequence
The generic concept for a (biological) sequence.
seqan3
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
std
SeqAn specific customisations in the standard namespace.
record.hpp
Provides the seqan3::record template and the seqan3::field enum.
seqan3::record
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:235
seqan3::record::base_type
detail::transfer_template_args_onto_t< field_types, std::tuple > base_type
A specialisation of std::tuple.
Definition: record.hpp:259