forked from freebayes/freebayes
-
Notifications
You must be signed in to change notification settings - Fork 0
/
BedReader.cpp
75 lines (62 loc) · 2.11 KB
/
BedReader.cpp
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
#ifndef BEDREADER_CPP
#define BEDREADER_CPP
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <deque>
#include <map>
#include <iterator>
#include <algorithm>
#include <cmath>
#include "split.h"
#include "Utility.h"
#include "BedReader.h"
#include "../intervaltree/IntervalTree.h"
using namespace std;
vector<BedTarget> BedReader::entries(void) {
vector<BedTarget> entries;
if (!is_open()) {
cerr << "bed targets file is not open" << endl;
exit(1);
}
string line;
while (std::getline(*this, line)) {
vector<string> fields = split(line, " \t");
BedTarget entry(strip(fields[0]),
atoi(strip(fields[1]).c_str()),
atoi(strip(fields[2]).c_str()) - 1, // use inclusive format internally
(fields.size() >= 4) ? strip(fields[3]) : "");
entries.push_back(entry);
}
return entries;
}
bool BedReader::targetsContained(string& seq, long left, long right) {
vector<Interval<BedTarget*> > results;
intervals[seq].findContained(left, right, results);
return !results.empty();
}
bool BedReader::targetsOverlap(string& seq, long left, long right) {
vector<Interval<BedTarget*> > results;
intervals[seq].findOverlapping(left, right, results);
return !results.empty();
}
vector<BedTarget*> BedReader::targetsContaining(BedTarget& target) {
vector<Interval<BedTarget*> > results;
intervals[target.seq].findContained(target.left, target.right, results);
vector<BedTarget*> contained;
for (vector<Interval<BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
contained.push_back(r->value);
}
return contained;
}
vector<BedTarget*> BedReader::targetsOverlapping(BedTarget& target) {
vector<Interval<BedTarget*> > results;
intervals[target.seq].findOverlapping(target.left, target.right, results);
vector<BedTarget*> overlapping;
for (vector<Interval<BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
overlapping.push_back(r->value);
}
return overlapping;
}
#endif