/usr/include/vcflib/BedReader.h is in libvcflib-dev 1.0.0~rc1+dfsg1-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #ifndef BEDREADER_H
#define BEDREADER_H
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <deque>
#include <map>
#include <iterator>
#include <algorithm>
#include "IntervalTree.h"
#include "split.h"
using namespace std;
string strip(string const& str, char const* separators = " \t") {
string::size_type const first = str.find_first_not_of(separators);
return (first == string::npos) ? string()
: str.substr(first, str.find_last_not_of(separators) - first + 1);
}
void parseRegion(
string& region,
string& startSeq,
int& startPos,
int& stopPos) {
size_t foundFirstColon = region.find(":");
// we only have a single string, use the whole sequence as the target
if (foundFirstColon == string::npos) {
startSeq = region;
startPos = 0;
stopPos = -1;
} else {
startSeq = region.substr(0, foundFirstColon);
string sep = "..";
size_t foundRangeSep = region.find(sep, foundFirstColon);
if (foundRangeSep == string::npos) {
sep = "-";
foundRangeSep = region.find("-", foundFirstColon);
}
if (foundRangeSep == string::npos) {
startPos = atoi(region.substr(foundFirstColon + 1).c_str());
// differ from bamtools in this regard, in that we process only
// the specified position if a range isn't given
stopPos = startPos + 1;
} else {
startPos = atoi(region.substr(foundFirstColon + 1, foundRangeSep - foundFirstColon).c_str());
// if we have range sep specified, but no second number, read to the end of sequence
if (foundRangeSep + sep.size() != region.size()) {
stopPos = atoi(region.substr(foundRangeSep + sep.size()).c_str()); // end-exclusive, bed-format
} else {
//stopPos = reference.sequenceLength(startSeq);
stopPos = -1;
}
}
}
}
// stores the posiitional information of a bed target entry
class BedTarget {
public:
string seq; // sequence name
int left; // left position
int right; // right position, adjusted to 0-base
string desc; // descriptive information, target name typically
BedTarget(string s) {
parseRegion(s, seq, left, right);
}
BedTarget(string s, int l, int r, string d = "")
: seq(s)
, left(l)
, right(r)
, desc(d)
{ }
};
class BedReader {
bool _isOpen;
ifstream file;
public:
bool isOpen(void) { return _isOpen; }
vector<BedTarget> targets;
map<string, IntervalTree<BedTarget*> > intervals; // intervals by reference sequence
vector<BedTarget> entries(void) {
vector<BedTarget> entries;
if (!isOpen()) {
cerr << "bed targets file is not open" << endl;
exit(1);
}
string line;
while (std::getline(file, line)) {
vector<string> fields = split(line, " \t");
BedTarget entry(strip(fields[0]),
atoi(strip(fields[1]).c_str()),
atoi(strip(fields[2]).c_str()),
(fields.size() >= 4) ? strip(fields[3]) : "");
entries.push_back(entry);
}
return entries;
}
vector<BedTarget*> targetsContained(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*> 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;
}
BedReader(void)
: _isOpen(false)
{ }
BedReader(string& fname)
: _isOpen(false) {
open(fname);
}
void addTargets(vector<BedTarget>& targets) {
map<string, vector<Interval<BedTarget*> > > intervalsBySeq;
for (vector<BedTarget>::iterator t = targets.begin(); t != targets.end(); ++t) {
intervalsBySeq[t->seq].push_back(Interval<BedTarget*>(1 + t->left, t->right, &*t));
}
for (map<string, vector<Interval<BedTarget*> > >::iterator s = intervalsBySeq.begin(); s != intervalsBySeq.end(); ++s) {
intervals[s->first] = IntervalTree<BedTarget*>(s->second);
}
}
void open(const string& fname) {
file.open(fname.c_str());
_isOpen = true;
targets = entries();
map<string, vector<Interval<BedTarget*> > > intervalsBySeq;
for (vector<BedTarget>::iterator t = targets.begin(); t != targets.end(); ++t) {
intervalsBySeq[t->seq].push_back(Interval<BedTarget*>(1 + t->left, t->right, &*t));
}
for (map<string, vector<Interval<BedTarget*> > >::iterator s = intervalsBySeq.begin(); s != intervalsBySeq.end(); ++s) {
intervals[s->first] = IntervalTree<BedTarget*>(s->second);
}
}
};
#endif
|