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root/gclib/tophat_cpp/GTFToFasta.h
Revision: 165
Committed: Fri Feb 10 01:04:05 2012 UTC (8 years, 8 months ago) by gpertea
File size: 1306 byte(s)
Log Message:
sync back with Daehwan. Test bam_merge for memory leaks!

Line User Rev File contents
1 gpertea 165 //
2     // gtfToFasta.h
3     // TopHat
4     //
5     // Created by Harold Pimentel on 10/26/11.
6     // Copyright 2011 __MyCompanyName__. All rights reserved.
7     //
8    
9     #ifndef GTFToFasta_H
10     #define GTFToFasta_H
11    
12     #ifdef HAVE_CONFIG_H
13     #include <config.h>
14     #endif
15    
16     #include <cassert>
17     #include <cstdlib>
18     #include <cstring>
19     #include <fstream>
20     #include <iostream>
21     #include <map>
22     #include <string>
23     #include <sstream>
24     #include <utility>
25     #include <vector>
26    
27     #include "common.h"
28     #include "gff.h"
29     #include "GFaSeqGet.h"
30     #include "FastaTools.h"
31    
32     std::string get_exonic_sequence(GffObj *p_trans, FastaRecord *rec);
33    
34     class GTFToFasta {
35     public:
36     GTFToFasta(std::string gtf_fname, std::string genome_fname);
37     ~GTFToFasta();
38     void make_transcriptome(std::string out_fname);
39    
40     // for debugging
41     void print_mapping();
42     private:
43     GffReader gtfReader_;
44     GFaSeqGet genome_fhandle_;
45    
46     std::string gtf_fname_;
47     std::string genome_fname_;
48    
49     FILE* gtf_fhandle_;
50    
51     // "contig" => vector(index_of_gff_obj)
52     // typedef std::map<const char* , std::vector< size_t >* > ContigTransMap;
53     typedef std::map<std::string, std::vector< size_t >* > ContigTransMap;
54     ContigTransMap contigTransMap_;
55    
56     void transcript_map();
57    
58     GTFToFasta(); // Don't want anyone calling the constructor w/o options
59     };
60    
61     #endif

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