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1 /*****************************************************************************
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2 mergeBed.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 <vector>
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14 #include <algorithm>
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15 #include <numeric>
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16 #include <iostream>
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17 #include <fstream>
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18 #include <limits.h>
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19 #include <stdlib.h>
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20
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21 using namespace std;
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22
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23
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24 //************************************************
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25 // Class methods and elements
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26 //************************************************
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27 class BedMerge {
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28
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29 public:
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30
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31 // constructor
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32 BedMerge(string &bedFile, bool numEntries,
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33 int maxDistance, bool forceStrand,
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34 bool reportNames, bool reportScores, const string &scoreOp);
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35
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36 // destructor
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37 ~BedMerge(void);
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38
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39 void MergeBed();
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40 void MergeBedStranded();
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41
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42 private:
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43
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44 string _bedFile;
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45 bool _numEntries;
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46 bool _forceStrand;
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47 bool _reportNames;
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48 bool _reportScores;
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49 string _scoreOp;
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50 int _maxDistance;
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51 // instance of a bed file class.
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52 BedFile *_bed;
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53
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54 void Report(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount);
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55 void ReportStranded(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount, string strand);
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56 void ReportMergedNames(const vector<string> &names);
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57 void ReportMergedScores(const vector<string> &scores);
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58
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59 };
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