Commit 3b7da2fe authored by Yannis Duffourd's avatar Yannis Duffourd

first implementation

parent 05411fd2
#ifndef _CNVCALLERGPU_H #ifndef _CNVCALLERGPU_H
#define _CNVCALLERGPU_H #define _CNVCALLERGPU_H
#include <vector> #include <vector>
#include <map> #include <map>
#include <string> #include <string>
#include <htslib/sam.h> #include <htslib/sam.h>
class cnvCallerGPU class cnvCallerGPU
{ {
public: public:
cnvCallerGPU(); cnvCallerGPU();
cnvCallerGPU(std::string, std::string, std::string, std::string, std::string, int, int, double, int, int); cnvCallerGPU(std::string, std::string, std::string, std::string, std::string, int, int, double, int, int);
int mainLoop(); int mainLoop();
int getNbThread(); int getNbThread();
int getWindowSize(); int getWindowSize();
int getStepSize(); int getStepSize();
double getZscore(); double getZscore();
std::string getOutputFilePairs(); std::string getOutputFilePairs();
std::string getOutputFileSplit(); std::string getOutputFileSplit();
std::string getOutputFile(); std::string getOutputFile();
std::string getReferenceFile(); std::string getReferenceFile();
std::string getBamFile(); std::string getBamFile();
private : private :
std::string sampleName; std::string sampleName;
std::string inputBamFile; std::string inputBamFile;
std::string referenceFile; std::string referenceFile;
std::string outputFile; std::string outputFile;
std::string outputFilePairs; std::string outputFilePairs;
std::string outputFileSplit; std::string outputFileSplit;
std::map<std::string, std::map<int32_t, std::map<int32_t, int32_t>>> rawCounts; std::map<std::string, std::map<int32_t, std::map<int32_t, int32_t>>> rawCounts;
std::map<std::string, std::map<int32_t, std::map<int32_t, float>>> gcContent; std::map<std::string, std::map<int32_t, std::map<int32_t, float>>> gcContent;
std::map<std::string, std::map<int32_t,int32_t>> refDict; std::map<std::string, std::map<int32_t,int32_t>> refDict;
int depthThreshold; int depthThreshold;
int nbThread; int nbThread;
int loggingLevel; int loggingLevel;
int window; int window;
int step; int step;
double zscore; double zscore;
// method // method
int getGenome(); int getGenome();
void displayGenome(); void displayGenome();
int readBam(std::string, int32_t, int32_t); int readBam(std::string, int32_t, int32_t);
int bamParsingLauncher(); int bamParsingLauncher();
}; };
#endif #endif
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