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comparison BEDTools-Version-2.14.3/src/sortBed/sortBed.h @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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-1:000000000000 0:dfcd8b6c1bda
1 /*****************************************************************************
2 sortBed.h
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "bedFile.h"
13 #include <vector>
14 #include <algorithm>
15 #include <iostream>
16 #include <fstream>
17
18 using namespace std;
19
20
21 //************************************************
22 // Class methods and elements
23 //************************************************
24 class BedSort {
25
26 public:
27
28 // constructor
29 BedSort(string &);
30
31 // destructor
32 ~BedSort(void);
33
34 void SortBed(); // the default. sorts by chrom (asc.) then by start (asc.)
35 void SortBedBySizeAsc();
36 void SortBedBySizeDesc();
37 void SortBedByChromThenSizeAsc();
38 void SortBedByChromThenSizeDesc();
39 void SortBedByChromThenScoreAsc();
40 void SortBedByChromThenScoreDesc();
41
42 private:
43 string _bedFile;
44
45 // instance of a bed file class.
46 BedFile *_bed;
47
48 // methods
49
50 };