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#ifndef CODE_ChimericDetection
#define CODE_ChimericDetection
#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ChimericAlign.h"
#include "Genome.h"
class ReadAlign;
class ChimericDetection {
private:
Parameters &P;
ReadAlign *RA;
Transcript ***trAll;
uint nW, *nWinTr;
char** Read1;
Genome &outGen;
public:
vector <ChimericAlign> chimAligns;
ChimericDetection(Parameters &Pin, Transcript ***trAll, uint *nWinTr, char** Read1in, Genome &genomeIn, fstream *ostreamChimJunctionIn, ReadAlign *RA);
bool chimericDetectionMult(uint nWin, uint *readLength, int maxNonChimAlignScore, ReadAlign *PEunmergedRA);
fstream *ostreamChimJunction;
};
#endif
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