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
|
/*Copyright (C) 2015 Olivier Delaneau, Halit Ongen, Emmanouil T. Dermitzakis
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.*/
#ifndef _GENOMIC_REGION_H
#define _GENOMIC_REGION_H
#define POS_MIN 0000000000
#define POS_MAX 1000000000
#include <string>
#include <exception>
using namespace std;
class genomic_region {
public:
string chr;
unsigned int start;
unsigned int end;
genomic_region() {
chr = "NA";
start = POS_MIN;
end = POS_MAX;
}
genomic_region(string _chr, unsigned int _start, unsigned int _end) {
chr = _chr;
start = _start;
end = _end;
assert(start <= end);
}
genomic_region(genomic_region & gr, unsigned int window) {
chr = gr.chr;
if (window > gr.start) start = 0;
else start = gr.start - window;
end = gr.end + window;
assert(start <= end);
}
bool isSet () {
return (chr != "NA");
}
string get() {
ostringstream s2( stringstream::out );
s2 << chr;
if (start != POS_MIN || end != POS_MAX) s2 << ":" << start << "-" << end;
return s2.str();
}
bool set (string _chr, unsigned int _start, unsigned int _end) {
chr = _chr;
start = _start;
end = _end;
if (start > end) return false;
return true;
}
bool parse(string str) {
size_t split_point_chr = str.find_first_of(":");
size_t split_point_pos = str.find_first_of("-");
//
if (split_point_chr == string::npos && split_point_pos == string::npos) {
chr = str;
} else if (split_point_chr == string::npos && split_point_pos != string::npos) {
return false;
} else if (split_point_chr != string::npos && split_point_pos == string::npos) {
chr = str.substr(0, split_point_chr);
try {
start = std::stoi(str.substr(split_point_chr+1, string::npos));
end = std::stoi(str.substr(split_point_chr+1, string::npos));
} catch (const std::exception & e) {
return false;
}
} else {
chr = str.substr(0, split_point_chr);
try {
start = std::stoi(str.substr(split_point_chr+1, split_point_pos));
end = std::stoi(str.substr(split_point_pos+1, string::npos));
} catch (const std::exception & e) {
return false;
}
}
return true;
}
};
#endif
|
