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1 /*****************************************************************************
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2 slopBed.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
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13 #include "bedFile.h"
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14 #include "genomeFile.h"
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15
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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 #include <map>
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20 #include <cstdlib>
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21 #include <ctime>
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22 using namespace std;
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23
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24
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25 //************************************************
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26 // Class methods and elements
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27 //************************************************
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28 class BedSlop {
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29
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30 public:
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31
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32 // constructor
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33 BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
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34
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35 // destructor
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36 ~BedSlop(void);
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37
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38
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39
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40 private:
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41
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42 string _bedFile;
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43 string _genomeFile;
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44
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45 bool _forceStrand;
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46 float _leftSlop;
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47 float _rightSlop;
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48 bool _fractional;
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49
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50 BedFile *_bed;
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51 GenomeFile *_genome;
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52
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53 // methods
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54
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55 void SlopBed();
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56
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57 // method to add requested "slop" to a single BED entry
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58 void AddSlop(BED &bed, int leftSlop, int rightSlop);
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59 };
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