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1 /*****************************************************************************
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2 windowBed.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 WINDOWBED_H
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13 #define WINDOWBED_H
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14
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15 #include "api/BamReader.h"
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16 #include "api/BamWriter.h"
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17 #include "api/BamAux.h"
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18 using namespace BamTools;
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19
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20 #include "bedFile.h"
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21 #include <vector>
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22 #include <iostream>
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23 #include <fstream>
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24
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25 using namespace std;
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26
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27 //************************************************
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28 // Class methods and elements
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29 //************************************************
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30 class BedWindow {
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31
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32 public:
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33
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34 // constructor
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35 BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
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36 bool anyHit, bool noHit, bool writeCount, bool strandWindows,
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37 bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
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38
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39 // destructor
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40 ~BedWindow(void);
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41
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42 private:
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43
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44 string _bedAFile;
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45 string _bedBFile;
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46 bool _anyHit;
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47 bool _writeCount;
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48 int _leftSlop;
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49 int _rightSlop;
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50 bool _noHit;
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51 bool _strandWindows;
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52 bool _matchOnSameStrand;
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53 bool _matchOnDiffStrand;
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54 bool _bamInput;
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55 bool _bamOutput;
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56 bool _isUncompressedBam;
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57
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58 // instance of a bed file class.
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59 BedFile *_bedA, *_bedB;
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60
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61 // methods
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62 void WindowIntersectBed();
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63 void WindowIntersectBam(string bamFile);
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64 void FindWindowOverlaps(const BED &a, vector<BED> &hits);
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65 bool FindOneOrMoreWindowOverlaps(const BED &a);
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66 void AddWindow(const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd);
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67
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68 };
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69 #endif /* WINDOWBED_H */
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