Mercurial > repos > aaronquinlan > multi_intersect
diff BEDTools-Version-2.14.3/src/nucBed/nucBed.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/nucBed/nucBed.h Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,55 @@ +/***************************************************************************** + nucBed.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 NUCBED_H +#define NUCBED_H + +#include "bedFile.h" +#include "sequenceUtils.h" +#include "Fasta.h" +#include <vector> +#include <iostream> +#include <fstream> + +using namespace std; + +//************************************************ +// Class methods and elements +//************************************************ +class NucBed { + +public: + + // constructor + NucBed(string &dbFile, string &bedFile, bool printSeq, + bool hasPattern, const string &pattern, + bool forceStrand); + // destructor + ~NucBed(void); + + void ProfileDNA(); + + +private: + string _dbFile; + string _bedFile; + bool _printSeq; + bool _hasPattern; + string _pattern; + bool _forceStrand; + + // instance of a bed file class. + BedFile *_bed; + void PrintHeader(void); + void ReportDnaProfile(const BED& bed, const string &sequence, int seqLength); +}; + +#endif