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root/gclib/tophat_cpp/GTFToFasta.h
Revision: 165
Committed: Fri Feb 10 01:04:05 2012 UTC (8 years, 6 months ago) by gpertea
File size: 1306 byte(s)
Log Message:
sync back with Daehwan. Test bam_merge for memory leaks!

Line File contents
1 //
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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