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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 nucBed.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 #ifndef NUCBED_H
13 #define NUCBED_H
14
15 #include "bedFile.h"
16 #include "sequenceUtils.h"
17 #include "Fasta.h"
18 #include <vector>
19 #include <iostream>
20 #include <fstream>
21
22 using namespace std;
23
24 //************************************************
25 // Class methods and elements
26 //************************************************
27 class NucBed {
28
29 public:
30
31 // constructor
32 NucBed(string &dbFile, string &bedFile, bool printSeq,
33 bool hasPattern, const string &pattern,
34 bool forceStrand);
35 // destructor
36 ~NucBed(void);
37
38 void ProfileDNA();
39
40
41 private:
42 string _dbFile;
43 string _bedFile;
44 bool _printSeq;
45 bool _hasPattern;
46 string _pattern;
47 bool _forceStrand;
48
49 // instance of a bed file class.
50 BedFile *_bed;
51 void PrintHeader(void);
52 void ReportDnaProfile(const BED& bed, const string &sequence, int seqLength);
53 };
54
55 #endif