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1 /*****************************************************************************
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2 annotateBed.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 ANNOTATEBED_H
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13 #define ANNOTATEBED_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 <algorithm>
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18 #include <iostream>
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19 #include <iomanip>
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20 #include <fstream>
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21 #include <stdlib.h>
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22
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23 using namespace std;
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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 BedAnnotate {
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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 BedAnnotate(const string &mainFile, const vector<string> &annoFileNames,
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34 const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth);
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35
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36 // destructor
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37 ~BedAnnotate(void);
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38
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39 // annotate the master file with all of the annotation files.
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40 void AnnotateBed();
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41
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42 private:
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43
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44 // input files.
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45 string _mainFile;
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46 vector<string> _annoFileNames;
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47 vector<string> _annoTitles;
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48
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49 // instance of a bed file class.
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50 BedFile *_bed;
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51 vector<BedFile*> _annoFiles;
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52
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53 // do we care about strandedness when counting coverage?
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54 bool _sameStrand;
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55 bool _diffStrand;
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56
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57 bool _reportCounts;
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58 bool _reportBoth;
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59
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60 // private function for reporting coverage information
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61 void ReportAnnotations();
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62
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63 void OpenAnnoFiles();
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64
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65 void CloseAnnoFiles();
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66
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67 void PrintHeader();
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68
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69 void InitializeMainFile();
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70 };
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71 #endif /* ANNOTATEBED_H */
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