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1 /*****************************************************************************
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2 sortBed.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 <iostream>
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16 #include <fstream>
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17
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18 using namespace std;
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19
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20
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21 //************************************************
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22 // Class methods and elements
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23 //************************************************
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24 class BedSort {
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25
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26 public:
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27
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28 // constructor
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29 BedSort(string &);
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30
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31 // destructor
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32 ~BedSort(void);
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33
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34 void SortBed(); // the default. sorts by chrom (asc.) then by start (asc.)
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35 void SortBedBySizeAsc();
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36 void SortBedBySizeDesc();
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37 void SortBedByChromThenSizeAsc();
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38 void SortBedByChromThenSizeDesc();
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39 void SortBedByChromThenScoreAsc();
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40 void SortBedByChromThenScoreDesc();
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41
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42 private:
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43 string _bedFile;
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44
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45 // instance of a bed file class.
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46 BedFile *_bed;
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47
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48 // methods
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49
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50 };
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