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1 /*****************************************************************************
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2 fastaFromBed.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 FASTAFROMBED_H
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13 #define FASTAFROMBED_H
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14
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15 #include "bedFile.h"
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16 #include "sequenceUtils.h"
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17 #include "Fasta.h"
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18 #include <vector>
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19 #include <iostream>
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20 #include <fstream>
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21
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22 using namespace std;
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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 Bed2Fa {
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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 Bed2Fa(bool useName, const string &dbFile, const string &bedFile, const string &fastaOutFile,
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33 bool useFasta, bool useStrand);
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34
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35 // destructor
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36 ~Bed2Fa(void);
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37
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38 void ExtractDNA();
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39 void ReportDNA(const BED &bed, string &dna);
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40
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41
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42 private:
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43
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44 bool _useName;
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45 string _dbFile;
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46 string _bedFile;
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47 string _fastaOutFile;
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48 bool _useFasta;
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49 bool _useStrand;
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50
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51 // instance of a bed file class.
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52 BedFile *_bed;
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53 ostream *_faOut;
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54 };
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55
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56 #endif
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