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1 /*****************************************************************************
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2 subtractBed.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 #ifndef SUBTRACTBED_H
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13 #define SUBTRACTBED_H
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14
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15 #include "bedFile.h"
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16 #include <vector>
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17 #include <iostream>
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18 #include <fstream>
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19
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20 using namespace std;
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21
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22 //************************************************
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23 // Class methods and elements
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24 //************************************************
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25 class BedSubtract {
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26
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27 public:
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28
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29 // constructor
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30 BedSubtract(string &bedAFile, string &bedBFile, float overlapFraction, bool sameStrand, bool diffStrand);
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31
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32 // destructor
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33 ~BedSubtract(void);
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34
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35 private:
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36
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37 // processing variables
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38 string _bedAFile;
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39 string _bedBFile;
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40 float _overlapFraction;
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41 bool _sameStrand;
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42 bool _diffStrand;
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43
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44
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45 // instances of bed file class.
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46 BedFile *_bedA, *_bedB;
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47
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48 // methods
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49 void FindAndSubtractOverlaps(BED &a, vector<BED> &hits);
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50 void SubtractBed();
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51 };
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52
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53 #endif /* SUBTRACTBED_H */
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