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1 /*****************************************************************************
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2 linksBed.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 // Class methods and elements
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22 //************************************************
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23 class BedLinks {
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24
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25 public:
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26
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27 // constructor
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28 BedLinks(string &bedFile, string &base, string &org, string &db);
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29
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30 // destructor
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31 ~BedLinks(void);
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32
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33 private:
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34 string _bedFile;
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35 string _base;
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36 string _org;
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37 string _db;
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38
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39 // instance of a bed file class.
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40 BedFile *_bed;
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41
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42 void WriteURL(BED &bed, string &base);
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43 void CreateLinks(); // the default. sorts by chrom (asc.) then by start (asc.)
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44 };
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