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comparison BEDTools-Version-2.14.3/src/fastaFromBed/fastaFromBed.h @ 1:bec36315bd12 default tip

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author aaronquinlan
date Sat, 19 Nov 2011 14:17:03 -0500
parents dfcd8b6c1bda
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0:dfcd8b6c1bda 1:bec36315bd12
1 /*****************************************************************************
2 fastaFromBed.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 FASTAFROMBED_H
13 #define FASTAFROMBED_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 Bed2Fa {
28
29 public:
30
31 // constructor
32 Bed2Fa(bool useName, const string &dbFile, const string &bedFile, const string &fastaOutFile,
33 bool useFasta, bool useStrand);
34
35 // destructor
36 ~Bed2Fa(void);
37
38 void ExtractDNA();
39 void ReportDNA(const BED &bed, string &dna);
40
41
42 private:
43
44 bool _useName;
45 string _dbFile;
46 string _bedFile;
47 string _fastaOutFile;
48 bool _useFasta;
49 bool _useStrand;
50
51 // instance of a bed file class.
52 BedFile *_bed;
53 ostream *_faOut;
54 };
55
56 #endif