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1 /*****************************************************************************
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2 complementBed.h
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #include "bedFile.h"
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13 #include "genomeFile.h"
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14
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15 #include <vector>
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16 #include <bitset>
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17 #include <algorithm>
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18 #include <iostream>
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19 #include <fstream>
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20 #include <limits.h>
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21 #include <stdlib.h>
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22
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23 using namespace std;
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24
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25
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26 //************************************************
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27 // Class methods and elements
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28 //************************************************
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29 class BedComplement {
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30
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31 public:
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32
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33 // constructor
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34 BedComplement(string &bedFile, string &genomeFile);
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35
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36 // destructor
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37 ~BedComplement(void);
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38
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39 void ComplementBed();
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40
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41 private:
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42
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43 string _bedFile;
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44 string _genomeFile;
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45 BedFile *_bed;
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46 GenomeFile *_genome;
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47 };
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