Renaming into Galacs

Galacs.cu

+// cnvCaller.cu
+// Version : 1.1.0
+// Description : C++/CUDA kernels to compute information needed by cnvcallerGPU 
+// Author: Theo.Serralta@u-bourgogne.fr ; yannis.duffourd@u-bourgogne.fr ; anthony.auclair@u-bourgogne.fr
+
+#include <cuda_runtime.h>
+
+// Kernel to compute raw average depth
+__global__ void computeDepthKernel(int *depth_data, int seq_length, int window_size, int step_size, float *depth_results) {
+    int idx = threadIdx.x + blockIdx.x * blockDim.x;
+    if (idx < seq_length - window_size + 1) {
+        int pos_start = (idx * step_size);
+        int pos_end = pos_start + window_size;
+        int count_reads = 0;
+        for (int i = pos_start; i < pos_end; i++) {
+            count_reads += depth_data[i];
+        }
+        depth_results[idx] = static_cast<float>(count_reads) / window_size;
+    }
+}
+
+// NEED TO OPTIMIZE WITH 3RD DEGREE POLYNOME
+// Kernel to normalize depth using GC content and mappability
+__global__ void normalizeDepthKernel(float *depth_correction, float *gc_results, float *map_results, 
+                                     float mean_depth, float *gc_to_median, int seq_length, 
+                                     int window_size, int step_size, float *normalized_depth) {
+    int idx = threadIdx.x + blockIdx.x * blockDim.x;
+    
+    if (idx < seq_length - window_size + 1) {
+        float gc_value = gc_results[idx];
+        float map_value = map_results[idx];
+        float depth_value = depth_correction[idx];
+
+        // Récupérer la médiane du GC content
+        float gc_median = gc_to_median[(int)gc_value];
+
+        // Vérifier les valeurs pour éviter des erreurs (division par zéro)
+        if (gc_median != 0.0f && map_value != 0.0f) {
+            normalized_depth[idx] = (depth_value / map_value) * (mean_depth / gc_median);
+        } else {
+            normalized_depth[idx] = 0.0f;
+        }
+    }
+}
+
+// Kernel to compute GC content in a sliding window
+__global__ void computeGCKernel(char *seq_data, int seq_length, int window_size, int step_size, float *gc_results) {
+    int idx = threadIdx.x + blockIdx.x * blockDim.x;
+    
+    if (idx < seq_length - window_size + 1) {
+        int pos_start = (idx * step_size);
+        int pos_end = pos_start + window_size;
+        int gc_count = 0;
+
+        for (int i = pos_start; i < pos_end; ++i) {
+            char base = seq_data[i];
+            if (base == 'G' || base == 'C' || base == 'g' || base == 'c') {
+                gc_count++;
+            }
+        }
+
+        gc_results[idx] = (static_cast<float>(gc_count) / window_size) * 100.0f;
+    }
+}
+
+// Kernel to compute weighted average mappability
+__global__ void computeMappabilityKernel(float *map_data, int seq_length, int window_size, int step_size, float *map_results) {
+    int idx = threadIdx.x + blockIdx.x * blockDim.x;
+
+    if (idx < seq_length - window_size + 1) {
+        int pos_start = (idx * step_size);
+        int pos_end = pos_start + window_size;
+        float weighted_sum = 0.0f;
+        float total_weight = 0.0f;
+
+        for (int i = pos_start; i < pos_end; ++i) {
+            float weight = map_data[i];
+            weighted_sum += weight;
+            total_weight += 1.0f;
+        }
+
+        map_results[idx] = (total_weight > 0.0f) ? (weighted_sum / total_weight) : 0.0f;
+    }
+}
+
+// Kernel to compute Z-score
+__global__ void computeZScoreKernel(float *normalized_depth, float mean_ratio, float std_ratio, int seq_length, float *z_score_results) {
+    int idx = threadIdx.x + blockIdx.x * blockDim.x;
+    if (idx < seq_length) {
+        float value = normalized_depth[idx];
+        if (isinf(value) || isnan(value)) {
+            value = 0.0f;
+        }
+        z_score_results[idx] = (value - mean_ratio) / std_ratio;
+    }
+}
\ No newline at end of file

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