Mercurial > repos > aaronquinlan > multi_intersect

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dfcd8b6c1bda
1 /*****************************************************************************
2 mergeBed.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 <numeric>
16 #include <iostream>
17 #include <fstream>
18 #include <limits.h>
19 #include <stdlib.h>
20
21 using namespace std;
22
23
24 //************************************************
25 // Class methods and elements
26 //************************************************
27 class BedMerge {
28
29 public:
30
31 // constructor
32 BedMerge(string &bedFile, bool numEntries,
33 int maxDistance, bool forceStrand,
34 bool reportNames, bool reportScores, const string &scoreOp);
35
36 // destructor
37 ~BedMerge(void);
38
39 void MergeBed();
40 void MergeBedStranded();
41
42 private:
43
44 string _bedFile;
45 bool _numEntries;
46 bool _forceStrand;
47 bool _reportNames;
48 bool _reportScores;
49 string _scoreOp;
50 int _maxDistance;
51 // instance of a bed file class.
52 BedFile *_bed;
53
54 void Report(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount);
55 void ReportStranded(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount, string strand);
56 void ReportMergedNames(const vector<string> &names);
57 void ReportMergedScores(const vector<string> &scores);
58
59 };