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
|
// ==========================================================================
// Mason - A Read Simulator
// ==========================================================================
// 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>
// ==========================================================================
#include "methylation_levels.h"
// ----------------------------------------------------------------------------
// Function VariantMaterializer::_fixVariationLevels()
// ----------------------------------------------------------------------------
void fixVariationLevels(MethylationLevels & levels,
TRng & rng,
seqan2::Dna5String const & contig,
seqan2::String<std::pair<int, bool> > const & varPoints,
MethylationLevelSimulatorOptions const & options)
{
MethylationLevelSimulator methSim(rng, options);
seqan2::Shape<seqan2::Dna5> shape2, shape3;
resize(shape2, 2);
resize(shape3, 3);
for (unsigned i = 0; i < length(varPoints); ++i)
{
int pos = varPoints[i].first;
if (varPoints[i].second) // is SNP
{
if (pos > 2)
{
levels.forward[pos - 2] = levels.reverse[pos - 2] = '!';
methSim.handleTwoMer(levels, pos - 2, hash(shape2, iter(contig, pos - 2, seqan2::Standard())));
methSim.handleThreeMer(levels, pos - 2, hash(shape3, iter(contig, pos - 2, seqan2::Standard())));
}
if (pos > 1)
{
levels.forward[pos - 1] = levels.reverse[pos - 1] = '!';
methSim.handleTwoMer(levels, pos - 1, hash(shape2, iter(contig, pos - 1, seqan2::Standard())));
}
levels.forward[pos] = levels.reverse[pos] = '!';
if (pos + 1 < (int)length(contig))
{
levels.forward[pos + 1] = levels.reverse[pos + 1] = '!';
methSim.handleTwoMer(levels, pos, hash(shape2, iter(contig, pos, seqan2::Standard())));
}
if (pos + 2 < (int)length(contig))
{
levels.forward[pos + 2] = levels.reverse[pos + 2] = '!';
methSim.handleTwoMer(levels, pos + 1, hash(shape2, iter(contig, pos + 1, seqan2::Standard())));
methSim.handleThreeMer(levels, pos, hash(shape3, iter(contig, pos, seqan2::Standard())));
}
}
else // is no SNP but breakpoint
{
// TODO(holtgrew): Double-check for correctness, might recompute too much around breakpoints.
if (pos > 2)
{
levels.forward[pos - 2] = levels.reverse[pos - 2] = '!';
methSim.handleTwoMer(levels, pos - 2, hash(shape2, iter(contig, pos - 2, seqan2::Standard())));
methSim.handleThreeMer(levels, pos - 2, hash(shape3, iter(contig, pos - 2, seqan2::Standard())));
}
if (pos > 1)
{
levels.forward[pos - 1] = levels.reverse[pos - 1] = '!';
methSim.handleTwoMer(levels, pos - 1, hash(shape2, iter(contig, pos - 1, seqan2::Standard())));
}
levels.forward[pos] = levels.reverse[pos] = '!';
if (pos + 1 < (int)length(contig))
{
methSim.handleTwoMer(levels, pos, hash(shape2, iter(contig, pos, seqan2::Standard())));
levels.forward[pos + 1] = levels.reverse[pos + 1] = '!';
}
if (pos + 2 < (int)length(contig))
{
methSim.handleTwoMer(levels, pos + 1, hash(shape2, iter(contig, pos + 1, seqan2::Standard())));
methSim.handleThreeMer(levels, pos, hash(shape3, iter(contig, pos, seqan2::Standard())));
}
}
}
}
|
