complementBed.h 997 Bytes
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/*****************************************************************************
  complementBed.h

  (c) 2009 - Aaron Quinlan
  Hall Laboratory
  Department of Biochemistry and Molecular Genetics
  University of Virginia
  aaronquinlan@gmail.com

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  Licenced under the GNU General Public License 2.0 license.
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******************************************************************************/
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#include "bedFile.h"
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#include "GenomeFile.h"
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#include <vector>
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#include <bitset>
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#include <algorithm>
#include <iostream>
#include <fstream>
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#include <limits.h>
#include <stdlib.h>
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using namespace std;


//************************************************
// Class methods and elements
//************************************************
class BedComplement {

public:

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  // constructor
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  BedComplement(string &bedFile, string &genomeFile);
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  // destructor
  ~BedComplement(void);

  void ComplementBed();

private:
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    string _bedFile;
    string _genomeFile;
    BedFile *_bed;
    GenomeFile *_genome;
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};