/***************************************************************************** coverageBed.h (c) 2009 - Aaron Quinlan Hall Laboratory Department of Biochemistry and Molecular Genetics University of Virginia aaronquinlan@gmail.com Licenced under the GNU General Public License 2.0 license. ******************************************************************************/ #ifndef COVERAGEBED_H #define COVERAGEBED_H #include "bedFile.h" #include "BamReader.h" #include "BamAux.h" #include "BamAncillary.h" using namespace BamTools; #include #include #include #include #include #include using namespace std; //************************************************ // Class methods and elements //************************************************ class BedCoverage { public: // constructor BedCoverage(string &bedAFile, string &bedBFile, bool forceStrand, bool writeHistogram, bool bamInput, bool obeySplits, bool eachBase); // destructor ~BedCoverage(void); private: // input files. string _bedAFile; string _bedBFile; // instance of a bed file class. BedFile *_bedA, *_bedB; // do we care about strandedness when counting coverage? bool _forceStrand; // should we write a histogram for each feature in B? bool _writeHistogram; // are we dealing with BAM input for "A"? bool _bamInput; // should we split BED/BAM into discrete blocks? bool _obeySplits; // should discrete coverage be reported for each base in each feature? bool _eachBase; // private function for reporting coverage information void ReportCoverage(); void CollectCoverageBed(); void CollectCoverageBam(string bamFile); }; #endif /* COVERAGEBED_H */