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1 /*****************************************************************************
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2 intersectBed.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 #ifndef INTERSECTBED_H
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13 #define INTERSECTBED_H
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14
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15 #include "bedFile.h"
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16 // #include "BamReader.h"
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17 // #include "BamWriter.h"
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18 // #include "BamAncillary.h"
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19 // #include "BamAux.h"
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20 // using namespace BamTools;
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21
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22
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23 #include <vector>
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24 #include <queue>
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25 #include <iostream>
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26 #include <fstream>
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27 #include <stdlib.h>
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28 using namespace std;
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29
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30
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31
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32 class BedIntersect {
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33
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34 public:
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35
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36 // constructor
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37 BedIntersect(string bedAFile, string bedBFile, bool anyHit,
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38 bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap,
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39 float overlapFraction, bool noHit, bool writeCount, bool forceStrand,
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40 bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput);
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41
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42 // destructor
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43 ~BedIntersect(void);
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44
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45 private:
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46
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47 //------------------------------------------------
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48 // private attributes
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49 //------------------------------------------------
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50 string _bedAFile;
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51 string _bedBFile;
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52
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53 bool _writeA; // should the original A feature be reported?
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54 bool _writeB; // should the original B feature be reported?
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55 bool _writeOverlap;
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56 bool _writeAllOverlap;
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57
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58 bool _forceStrand;
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59 bool _reciprocal;
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60 float _overlapFraction;
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61
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62 bool _anyHit;
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63 bool _noHit;
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64 bool _writeCount; // do we want a count of the number of overlaps in B?
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65 bool _obeySplits;
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66 bool _bamInput;
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67 bool _bamOutput;
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68
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69 bool _printable;
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70
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71 queue<BED*> _outputBuffer;
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72 bool _lastPick;
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73
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74 map<string, vector<BED*> > _windowA;
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75 map<string, vector<BED*> > _windowB;
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76
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77 // instance of a bed file class.
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78 BedFile *_bedA, *_bedB;
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79
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80 //------------------------------------------------
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81 // private methods
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82 //------------------------------------------------
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83 void IntersectBed(istream &bedInput);
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84
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85 void Scan(BED *x, vector<BED *> *windowX, BedLineStatus xStatus,
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86 const BED &y, vector<BED *> *windowY, BedLineStatus yStatus);
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87
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88 void AddHits(BED *x, const BED &y);
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89
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90 void FlushOutputBuffer(bool final = false);
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91
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92 vector<BED*>* GetWindow(const string &chrom, bool isA);
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93
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94 void ChromSwitch(const string &chrom);
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95
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96 void IntersectBed();
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97
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98 void IntersectBam(string bamFile);
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99
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100 bool processHits(BED &a, vector<BED> &hits);
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101
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102 bool FindOverlaps(const BED &a, vector<BED> &hits);
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103
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104 bool FindOneOrMoreOverlap(const BED &a);
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105
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106 void ReportOverlapDetail(const int &overlapBases, const BED &a, const BED &b,
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107 const CHRPOS &s, const CHRPOS &e);
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108 void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
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109
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110 void ReportHits(set<BED> &A, set<BED> &B);
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111
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112 };
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113
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114 #endif /* INTERSECTBED_H */
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