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
|
/*
@copyright 2016-2021 Clarity Genomics BVBA
@copyright 2012-2016 Bonsai Bioinformatics Research Group
@copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
@parblock
SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
This is a free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
SortMeRNA is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
@endparblock
@contributors Jenya Kopylova jenya.kopylov@gmail.com
Laurent No laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikal Salson mikael.salson@lifl.fr
Hlne Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/**
* file: ssw.hpp
* created: Oct 28, 2017 Sat
*/
#pragma once
#include <stdint.h>
#include <vector>
#include <iterator>
typedef struct s_align2 {
std::vector<uint32_t> cigar;
uint32_t ref_num; // position of the sequence in the reference file [0...number of sequences in the ref.file - 1]
int32_t ref_begin1;
int32_t ref_end1;
int32_t read_begin1;
int32_t read_end1;
uint32_t readlen;
uint16_t score1; // <- 'ssw.c::ssw_align'
uint16_t part;
uint16_t index_num;
bool strand; // flags whether this alignment was done on a forward (true) or reverse-complement (false) read.
// default construct
s_align2() : ref_num(0), ref_begin1(0), ref_end1(0), read_begin1(0), read_end1(0), readlen(0), score1(0), part(0), index_num(0), strand(false) {}
// construct from binary string
s_align2(std::string bstr)
{
size_t offset = 0;
size_t len = 0; // cigar, refname length
// cannot use copy/copy_n - VC error C4996: 'std::copy_n::_Unchecked_iterators
std::memcpy(static_cast<void*>(&len), bstr.data(), sizeof(len));
offset += sizeof(len);
cigar.assign(len, 0);
std::memcpy(static_cast<void*>(cigar.data()), bstr.data() + offset, len * sizeof(uint32_t));
offset += len * sizeof(uint32_t);
// ref_num
std::memcpy(static_cast<void*>(&ref_num), bstr.data() + offset, sizeof(ref_num));
offset += sizeof(ref_num);
// ref_begin1
std::memcpy(static_cast<void*>(&ref_begin1), bstr.data() + offset, sizeof(ref_begin1));
offset += sizeof(ref_begin1);
// ref_end1
std::memcpy(static_cast<void*>(&ref_end1), bstr.data() + offset, sizeof(ref_end1));
offset += sizeof(ref_end1);
// read_begin1
std::memcpy(static_cast<void*>(&read_begin1), bstr.data() + offset, sizeof(read_begin1));
offset += sizeof(read_begin1);
// read_end1
std::memcpy(static_cast<void*>(&read_end1), bstr.data() + offset, sizeof(read_end1));
offset += sizeof(read_end1);
// readlen
std::memcpy(static_cast<void*>(&readlen), bstr.data() + offset, sizeof(readlen));
offset += sizeof(readlen);
// score1
std::memcpy(static_cast<void*>(&score1), bstr.data() + offset, sizeof(score1));
offset += sizeof(score1);
// part
std::memcpy(static_cast<void*>(&part), bstr.data() + offset, sizeof(part));
offset += sizeof(part);
// index_num
std::memcpy(static_cast<void*>(&index_num), bstr.data() + offset, sizeof(index_num));
offset += sizeof(index_num);
// strand
std::memcpy(static_cast<void*>(&strand), bstr.data() + offset, sizeof(strand));
offset += sizeof(strand);
}
// convert to binary string
std::string toString()
{
std::string buf;
// length of cigar
size_t cigarlen = cigar.size();
char* beginIt = static_cast<char*>(static_cast<void*>(&cigarlen));
std::copy_n(beginIt, sizeof(cigarlen), std::back_inserter(buf));
// cigar
beginIt = static_cast<char*>(static_cast<void*>(cigar.data()));
std::copy_n(beginIt, cigarlen * sizeof(cigar[0]), std::back_inserter(buf));
beginIt = static_cast<char*>(static_cast<void*>(&ref_num));
std::copy_n(beginIt, sizeof(ref_num), std::back_inserter(buf)); // ref_num
beginIt = static_cast<char*>(static_cast<void*>(&ref_begin1));
std::copy_n(beginIt, sizeof(ref_begin1), std::back_inserter(buf)); // ref_begin1
beginIt = static_cast<char*>(static_cast<void*>(&ref_end1));
std::copy_n(beginIt, sizeof(ref_end1), std::back_inserter(buf)); // ref_end1
beginIt = static_cast<char*>(static_cast<void*>(&read_begin1));
std::copy_n(beginIt, sizeof(read_begin1), std::back_inserter(buf)); // read_begin1
beginIt = static_cast<char*>(static_cast<void*>(&read_end1));
std::copy_n(beginIt, sizeof(read_end1), std::back_inserter(buf)); // read_end1
beginIt = static_cast<char*>(static_cast<void*>(&readlen));
std::copy_n(beginIt, sizeof(readlen), std::back_inserter(buf)); // readlen
beginIt = static_cast<char*>(static_cast<void*>(&score1));
std::copy_n(beginIt, sizeof(score1), std::back_inserter(buf)); // score1
beginIt = static_cast<char*>(static_cast<void*>(&part));
std::copy_n(beginIt, sizeof(part), std::back_inserter(buf)); // part
beginIt = static_cast<char*>(static_cast<void*>(&index_num));
std::copy_n(beginIt, sizeof(index_num), std::back_inserter(buf)); // index_num
// strand
beginIt = static_cast<char*>(static_cast<void*>(&strand));
std::copy_n(beginIt, sizeof(strand), std::back_inserter(buf));
return buf;
} // ~toString
// for serialization
size_t size() {
return sizeof(uint32_t) * cigar.size()
+ sizeof(ref_num)
+ sizeof(ref_begin1)
+ sizeof(ref_end1)
+ sizeof(read_begin1)
+ sizeof(read_end1)
+ sizeof(readlen)
+ sizeof(score1)
+ sizeof(part)
+ sizeof(index_num)
+ sizeof(strand);
}
bool operator==(const s_align2& other)
{
return other.cigar == cigar &&
other.ref_num == ref_num &&
other.ref_begin1 == ref_begin1 &&
other.ref_end1 == ref_end1 &&
other.read_begin1 == read_begin1 &&
other.read_end1 == read_end1 &&
other.readlen == readlen &&
other.score1 == score1 &&
other.part == part &&
other.index_num == index_num &&
other.strand == strand;
}
} s_align2;
|
