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