Mercurial > repos > aaronquinlan > multi_intersect
diff BEDTools-Version-2.14.3/src/subtractBed/subtractBed.h @ 0:dfcd8b6c1bda
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author | aaronquinlan |
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date | Thu, 03 Nov 2011 10:25:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/subtractBed/subtractBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,53 @@ +/***************************************************************************** + subtractBed.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 SUBTRACTBED_H +#define SUBTRACTBED_H + +#include "bedFile.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class BedSubtract { + +public: + + // constructor + BedSubtract(string &bedAFile, string &bedBFile, float overlapFraction, bool sameStrand, bool diffStrand); + + // destructor + ~BedSubtract(void); + +private: + + // processing variables + string _bedAFile; + string _bedBFile; + float _overlapFraction; + bool _sameStrand; + bool _diffStrand; + + + // instances of bed file class. + BedFile *_bedA, *_bedB; + + // methods + void FindAndSubtractOverlaps(BED &a, vector<BED> &hits); + void SubtractBed(); +}; + +#endif /* SUBTRACTBED_H */