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

first implementation

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