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1 /*****************************************************************************
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2 genomeCoverage.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 "BamAncillary.h"
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16 #include "api/BamReader.h"
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17 #include "api/BamAux.h"
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18 using namespace BamTools;
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19
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20 #include <vector>
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21 #include <set>
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22 #include <iostream>
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23 #include <fstream>
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24 using namespace std;
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25
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26
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27 //***********************************************
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28 // Typedefs
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29 //***********************************************
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30 typedef map<int, DEPTH, less<int> > depthMap;
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31 typedef map<string, depthMap, less<string> > chromDepthMap;
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32
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33 typedef map<int, unsigned int, less<int> > histMap;
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34 typedef map<string, histMap, less<string> > chromHistMap;
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35
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36 //************************************************
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37 // Class methods and elements
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38 //************************************************
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39 class BedGenomeCoverage {
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40
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41 public:
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42
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43 // constructor
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44 BedGenomeCoverage(string bedFile, string genomeFile,
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45 bool eachBase, bool startSites,
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46 bool bedGraph, bool bedGraphAll,
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47 int max, float scale,
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48 bool bamInput, bool obeySplits,
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49 bool filterByStrand, string requestedStrand,
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50 bool only_5p_end, bool only_3p_end,
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51 bool eachBaseZeroBased,
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52 bool add_gb_track_line, string gb_track_line_opts);
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53
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54 // destructor
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55 ~BedGenomeCoverage(void);
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56
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57 private:
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58
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59 // data (parms)
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60 string _bedFile;
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61 string _genomeFile;
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62 bool _bamInput;
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63 bool _eachBase;
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64 bool _eachBaseZeroBased;
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65 bool _startSites;
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66 bool _bedGraph;
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67 bool _bedGraphAll;
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68 int _max;
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69 float _scale;
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70 bool _obeySplits;
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71 bool _filterByStrand;
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72 bool _only_5p_end;
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73 bool _only_3p_end;
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74 bool _add_gb_track_line;
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75 string _gb_track_line_opts;
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76 string _requestedStrand;
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77
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78 BedFile *_bed;
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79 GenomeFile *_genome;
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80
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81 // data for internal processing
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82 chromDepthMap _chromCov;
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83 string _currChromName ;
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84 vector<DEPTH> _currChromCoverage;
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85 chromHistMap _currChromDepthHist;
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86 int _currChromSize ;
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87 set<string> _visitedChromosomes;
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88
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89
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90 // methods
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91 void CoverageBed();
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92 void CoverageBam(string bamFile);
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93 void LoadBamHeaderIntoGenomeFile(const string &bamFile);
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94 void ReportChromCoverage(const vector<DEPTH> &, const int &chromSize, const string &chrom, chromHistMap&);
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95 void ReportGenomeCoverage(chromHistMap &chromDepthHist);
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96 void ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, const int &chromSize, const string &chrom);
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97 void ResetChromCoverage();
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98 void StartNewChrom (const string& chrom);
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99 void AddCoverage (int start, int end);
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100 void AddBlockedCoverage(const vector<BED> &bedBlocks);
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101 void PrintFinalCoverage();
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102 void PrintTrackDefinitionLine();
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103 };
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104
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