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1 /*****************************************************************************
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2 maskFastaFromBed.h
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3 (c) 2009 - Aaron Quinlan
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4 Hall Laboratory
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5 Department of Biochemistry and Molecular Genetics
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6 University of Virginia
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7 aaronquinlan@gmail.com
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8
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9 Licenced under the GNU General Public License 2.0 license.
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10 ******************************************************************************/
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11 #ifndef MASKFASTAFROMBED_H
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12 #define MASKFASTAFROMBED_H
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13
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14 #include "bedFile.h"
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15 #include "sequenceUtils.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 #include <cctype> /* for tolower */
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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 // Class methods and elements
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25 //************************************************
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26 class MaskFastaFromBed {
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27
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28 public:
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29
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30 // constructor
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31 MaskFastaFromBed(const string &fastaInFile, const string &bedFile,
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32 const string &fastaOutFile, bool softMask, char maskChar);
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33
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34 // destructor
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35 ~MaskFastaFromBed(void);
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36
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37
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38 private:
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39
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40 bool _softMask;
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41
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42 string _fastaInFile;
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43 string _bedFile;
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44 string _fastaOutFile;
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45 char _maskChar; // typically "N", but user's can choose something else, e.g., "X"
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46
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47 // instance of a bed file class.
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48 BedFile *_bed;
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49
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50 void MaskFasta();
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51
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52 void PrettyPrintChrom(ofstream &out, string chrom, const string &sequence, int width);
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53
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54 };
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55
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56 #endif /* MASKFASTAFROMBED */
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