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#ifndef H_GTF
#define H_GTF
#include "IncludeDefine.h"
#include "Parameters.h"
#include "SjdbClass.h"
#include "Genome.h"
#include "SuperTranscriptome.h"
class GTF {
private:
Genome &genome;
Parameters &P;
string dirOut;
SjdbClass &sjdbLoci;
public:
bool gtfYes;
enum {exT,exS,exE,exG,exL}; //indexes in the exonLoci array
uint64 exonN;
vector<array<uint64,exL>> exonLoci;
vector<uint32> transcriptStrand;
vector <string> transcriptID, geneID;
vector<array<string,2>> geneAttr;
vector<vector<uint8>> transcriptSeq;//sequences of normal transcripts
vector<array<uint64,2>> transcriptStartEnd;//normal transcripts start/end in the normal genome
SuperTranscriptome superTrome;
GTF(Genome &genomeIn, Parameters &Pin, const string &dirOut, SjdbClass &sjdbLoci);
uint64 transcriptGeneSJ(const string &dirOut);
void superTranscript();
};
#endif
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