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1 /*****************************************************************************
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2 genomeFile.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 Licensed under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #ifndef GENOMEFILE_H
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13 #define GENOMEFILE_H
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14
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15 #include <map>
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16 #include <string>
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17 #include <iostream>
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18 #include <sstream>
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19 #include <fstream>
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20 #include <cstring>
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21 #include <cstdio>
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22 #include "api/BamReader.h"
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23 #include "api/BamAux.h"
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24 using namespace BamTools;
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25
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26 using namespace std;
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27
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28
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29 // typedef for mapping b/w chrom name and it's size in b.p.
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30 typedef map<string, int, std::less<string> > chromToSizes;
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31
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32
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33 class GenomeFile {
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34
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35 public:
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36
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37 // Constructor using a file
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38 GenomeFile(const string &genomeFile);
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39
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40 // Constructor using a vector of BamTools RefVector
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41 GenomeFile(const RefVector &genome);
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42
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43 // Destructor
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44 ~GenomeFile(void);
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45
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46 // load a GENOME file into a map keyed by chrom. value is size of chrom.
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47 void loadGenomeFileIntoMap();
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48
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49 int getChromSize(const string &chrom); // return the size of a chromosome
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50 vector<string> getChromList(); // return a list of chrom names
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51 int getNumberOfChroms(); // return the number of chroms
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52 string getGenomeFileName(); // return the name of the genome file
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53
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54
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55
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56 private:
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57 string _genomeFile;
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58 chromToSizes _chromSizes;
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59 vector<string> _chromList;
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60 };
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61
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62 #endif /* GENOMEFILE_H */
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