1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
#ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_H_
#define INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_H_
#include <map>
#include <vector>
#include <stdexcept>
#include <seqan/store.h>
#include "consensus_alignment_options.h"
#include "consensus_builder.h"
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class ConsensusAlignerIllegalArgumentException
// ----------------------------------------------------------------------------
/*!
* @class ConsensusAlignerIllegalArgumentException
* @headerfile <seqan/consensus.h>
* @brief Thrown in ConsensusAlignerInputException on invalid arguments.
*
* @signature class ConsensusAlignerException;
*/
class ConsensusAlignerException : public std::runtime_error
{
public:
explicit ConsensusAlignerException(std::string const & whatArg) : std::runtime_error(whatArg)
{}
};
// ----------------------------------------------------------------------------
// Class ConsensusAligner_
// ----------------------------------------------------------------------------
// Implementation helper of the consensusAlignment() function.
template <typename TFragmentStore>
class ConsensusAligner_
{
public:
ConsensusAligner_(TFragmentStore & store, ConsensusAlignmentOptions const & options) :
store(store), options(options)
{}
void run();
private:
// Checks that there is at most one alignment per read in the store.
void checkAlignmentMultiplicity() const;
// Normalize reverse-complemented alignments and store the read IDs in rcIDs.
void normalizeRCReads();
// Restore read orientation of RC reads again.
void restoreRCReads();
// The ids of the reads that had a reverse-complemented alignment.
std::set<unsigned> rcIDs;
// The FragmentStore to use for consensus computation.
TFragmentStore & store;
// The configuration of the consensus alignment.
ConsensusAlignmentOptions const & options;
};
template <typename TFragmentStore>
inline void ConsensusAligner_<TFragmentStore>::normalizeRCReads()
{
for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
if (store.alignedReadStore[i].beginPos > store.alignedReadStore[i].endPos)
{
unsigned readID = store.alignedReadStore[i].readId;
rcIDs.insert(readID);
reverseComplement(store.readSeqStore[readID]);
std::swap(store.alignedReadStore[i].beginPos, store.alignedReadStore[i].endPos);
}
}
template <typename TFragmentStore>
inline void ConsensusAligner_<TFragmentStore>::restoreRCReads()
{
for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
{
unsigned readID = store.alignedReadStore[i].readId;
if (rcIDs.count(readID))
{
std::swap(store.alignedReadStore[i].beginPos, store.alignedReadStore[i].endPos);
reverseComplement(store.readSeqStore[readID]);
}
}
}
template <typename TFragmentStore>
inline void ConsensusAligner_<TFragmentStore>::checkAlignmentMultiplicity() const
{
std::set<unsigned> seen;
for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
if (seen.count(store.alignedReadStore[i].readId))
throw ConsensusAlignerException("Read with id has more than one alignment.");
else
seen.insert(store.alignedReadStore[i].readId);
}
template <typename TFragmentStore>
inline void ConsensusAligner_<TFragmentStore>::run()
{
// Check that there only is one alignment per read and escape via exception otherwise.
checkAlignmentMultiplicity();
// Normalize reads with RC alignment.
normalizeRCReads();
if (options.verbosity >= 1)
std::cerr << "computing overlap infos...\n";
// Build overlap infos, based on position and contig ID if configured to do so.
std::vector<OverlapInfo_> overlapInfos;
OverlapInfoComputation_<TFragmentStore> ovlInfoHelper(store, options);
ovlInfoHelper.run(overlapInfos);
if (options.verbosity >= 1)
std::cerr << "=> " << overlapInfos.size() << " overlap infos\n";
// TODO(holtgrew): Pick pairwise best alignments.
if (options.verbosity >= 1)
std::cerr << "building consensus...\n";
// Consensus builder.
ConsensusBuilder_<TFragmentStore> consBuilder(options);
consBuilder.run(store, overlapInfos);
// Restore RC'ed reads.
restoreRCReads();
}
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
} // namespace seqan2
#endif // #ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_H_
|
