first implementation

Galacs.h

-#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