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comparison BEDTools-Version-2.14.3/src/shuffleBed/shuffleBed.h @ 1:bec36315bd12 default tip

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author aaronquinlan
date Sat, 19 Nov 2011 14:17:03 -0500
parents dfcd8b6c1bda
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0:dfcd8b6c1bda 1:bec36315bd12
1 /*****************************************************************************
2 shuffleBed.h
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "bedFile.h"
13 #include "genomeFile.h"
14
15 #include <vector>
16 #include <iostream>
17 #include <fstream>
18 #include <map>
19 #include <cstdlib>
20 #include <ctime>
21 #include <sys/time.h>
22 #include <unistd.h>
23 #include <sys/types.h>
24 using namespace std;
25
26 const int MAX_TRIES = 1000000;
27
28 //************************************************
29 // Class methods and elements
30 //************************************************
31 class BedShuffle {
32
33 public:
34
35 // constructor
36 BedShuffle(string &bedFile, string &genomeFile, string &excludeFile, string &includeFile,
37 bool haveSeed, bool haveExclude, bool haveInclude, bool sameChrom,
38 float overlapFraction, int seed);
39
40 // destructor
41 ~BedShuffle(void);
42
43 private:
44
45 string _bedFile;
46 string _genomeFile;
47 string _excludeFile;
48 string _includeFile;
49 float _overlapFraction;
50 int _seed;
51 bool _sameChrom;
52 bool _haveExclude;
53 bool _haveInclude;
54 bool _haveSeed;
55
56
57 // The BED file from which to compute coverage.
58 BedFile *_bed;
59 BedFile *_exclude;
60 BedFile *_include;
61
62 GenomeFile *_genome;
63
64 vector<string> _chroms;
65 int _numChroms;
66 vector<string> _includeChroms;
67 int _numIncludeChroms;
68
69 // methods
70 void Shuffle();
71 void ShuffleWithExclusions();
72 void ShuffleWithInclusions();
73
74 void ChooseLocus(BED &);
75 void ChooseLocusFromInclusionFile(BED &);
76 };