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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 coverageBed.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 #ifndef COVERAGEBED_H
13 #define COVERAGEBED_H
14
15 #include "bedFile.h"
16
17 #include "api/BamReader.h"
18 #include "api/BamAux.h"
19 #include "BamAncillary.h"
20 using namespace BamTools;
21
22 #include <vector>
23 #include <algorithm>
24 #include <iostream>
25 #include <iomanip>
26 #include <fstream>
27 #include <stdlib.h>
28
29 using namespace std;
30
31 //************************************************
32 // Class methods and elements
33 //************************************************
34 class BedCoverage {
35
36 public:
37
38 // constructor
39 BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand, bool writeHistogram,
40 bool bamInput, bool obeySplits, bool eachBase, bool countsOnly);
41
42 // destructor
43 ~BedCoverage(void);
44
45 private:
46
47 // input files.
48 string _bedAFile;
49 string _bedBFile;
50
51 // instance of a bed file class.
52 BedFile *_bedA, *_bedB;
53
54 // do we care about same or opposite strandedness when counting coverage?
55 bool _sameStrand;
56 bool _diffStrand;
57
58 // should we write a histogram for each feature in B?
59 bool _writeHistogram;
60
61 // are we dealing with BAM input for "A"?
62 bool _bamInput;
63
64 // should we split BED/BAM into discrete blocks?
65 bool _obeySplits;
66
67 // should discrete coverage be reported for each base in each feature?
68 bool _eachBase;
69
70 // should we just count overlaps and not try to describe the breadth?
71 bool _countsOnly;
72
73 // private function for reporting coverage information
74 void ReportCoverage();
75
76 // private function for reporting overlap counts
77 void ReportCounts();
78
79 void CollectCoverageBed();
80
81 void CollectCoverageBam(string bamFile);
82 };
83 #endif /* COVERAGEBED_H */