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comparison BEDTools-Version-2.14.3/src/genomeCoverageBed/genomeCoverageBed.h @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 genomeCoverage.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 "BamAncillary.h"
16 #include "api/BamReader.h"
17 #include "api/BamAux.h"
18 using namespace BamTools;
19
20 #include <vector>
21 #include <set>
22 #include <iostream>
23 #include <fstream>
24 using namespace std;
25
26
27 //***********************************************
28 // Typedefs
29 //***********************************************
30 typedef map<int, DEPTH, less<int> > depthMap;
31 typedef map<string, depthMap, less<string> > chromDepthMap;
32
33 typedef map<int, unsigned int, less<int> > histMap;
34 typedef map<string, histMap, less<string> > chromHistMap;
35
36 //************************************************
37 // Class methods and elements
38 //************************************************
39 class BedGenomeCoverage {
40
41 public:
42
43 // constructor
44 BedGenomeCoverage(string bedFile, string genomeFile,
45 bool eachBase, bool startSites,
46 bool bedGraph, bool bedGraphAll,
47 int max, float scale,
48 bool bamInput, bool obeySplits,
49 bool filterByStrand, string requestedStrand,
50 bool only_5p_end, bool only_3p_end,
51 bool eachBaseZeroBased,
52 bool add_gb_track_line, string gb_track_line_opts);
53
54 // destructor
55 ~BedGenomeCoverage(void);
56
57 private:
58
59 // data (parms)
60 string _bedFile;
61 string _genomeFile;
62 bool _bamInput;
63 bool _eachBase;
64 bool _eachBaseZeroBased;
65 bool _startSites;
66 bool _bedGraph;
67 bool _bedGraphAll;
68 int _max;
69 float _scale;
70 bool _obeySplits;
71 bool _filterByStrand;
72 bool _only_5p_end;
73 bool _only_3p_end;
74 bool _add_gb_track_line;
75 string _gb_track_line_opts;
76 string _requestedStrand;
77
78 BedFile *_bed;
79 GenomeFile *_genome;
80
81 // data for internal processing
82 chromDepthMap _chromCov;
83 string _currChromName ;
84 vector<DEPTH> _currChromCoverage;
85 chromHistMap _currChromDepthHist;
86 int _currChromSize ;
87 set<string> _visitedChromosomes;
88
89
90 // methods
91 void CoverageBed();
92 void CoverageBam(string bamFile);
93 void LoadBamHeaderIntoGenomeFile(const string &bamFile);
94 void ReportChromCoverage(const vector<DEPTH> &, const int &chromSize, const string &chrom, chromHistMap&);
95 void ReportGenomeCoverage(chromHistMap &chromDepthHist);
96 void ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, const int &chromSize, const string &chrom);
97 void ResetChromCoverage();
98 void StartNewChrom (const string& chrom);
99 void AddCoverage (int start, int end);
100 void AddBlockedCoverage(const vector<BED> &bedBlocks);
101 void PrintFinalCoverage();
102 void PrintTrackDefinitionLine();
103 };
104