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1 /*****************************************************************************
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2 closestBed.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 CLOSESTBED_H
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13 #define CLOSESTBED_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 BedClosest {
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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 BedClosest(string &bedAFile, string &bedBFile,
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31 bool sameStrand, bool diffStrand, string &tieMode,
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32 bool reportDistance, bool signDistance, string &strandedDistMode,
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33 bool ignoreOverlaps);
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34
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35 // destructor
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36 ~BedClosest(void);
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37
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38 // find the closest feature in B to A
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39 void FindClosestBed();
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40
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41 private:
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42
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43 // data
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44 string _bedAFile;
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45 string _bedBFile;
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46 string _tieMode;
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47 bool _sameStrand;
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48 bool _diffStrand;
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49 bool _reportDistance;
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50 bool _signDistance;
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51 string _strandedDistMode;
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52 bool _ignoreOverlaps;
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53
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54 BedFile *_bedA, *_bedB;
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55
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56 // methods
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57 void reportNullB();
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58 void FindWindowOverlaps(BED &, vector<BED> &);
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59
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60 };
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61 #endif /* CLOSEST_H */
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