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#ifndef H_SuperTranscriptome
#define H_SuperTranscriptome
#include "IncludeDefine.h"
#include "Parameters.h"
struct sjInfo {
uint32 start;
uint32 end;
uint32 tr;
uint32 super;
};
class SuperTranscript {//one supertranscript
public:
uint8 *seqP;//pointer to sequence
uint32 length;
vector<array<uint32,3>> sjC;//collapsed junctions
vector<uint32> sjDonor;//SJ donor coordinates, sorted
};
class SuperTranscriptome {
private:
Parameters &P;
public:
vector<uint8> seqConcat;//concatenated sequences of supertranscripts, a.k.a. Condensed Genome
vector<vector<uint8>> seq;//sequences of supertranscripts
vector<uint64> trIndex;//superTr's index this tr belongs to
vector<array<uint64,2>> trStartEnd;//tr start/end in the superTr it belongs to
vector<sjInfo> sj;//all junctions
vector<SuperTranscript> superTrs;
uint32 sjNmax, sjDonorNmax;//max number of SJs per superTr, SJ donors
uint32 N; //number of superTr
SuperTranscriptome(Parameters &P) : P(P) {};
void sjCollapse();
void load(char *G, vector<uint64> &chrStart, vector<uint64> &chrLength);
};
#endif
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