bug fixes on file read

theLongLab · Oct 2, 2024 · d9343f4 · d9343f4
1 parent 5f00f37
commit d9343f4
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Showing 7 changed files with 1,041 additions and 976 deletions.
diff --git a/cancer.cu b/cancer.cu
@@ -114,6 +114,8 @@ cancer::cancer(string parameter_Master_Location)
         cout << "Decimal date: " << stop_Date << endl;
     }
 
+    // exit(-1);
+
     cout << "\nConfiguring hardware resources:\n\n";
     this->CPU_cores = Parameters.get_INT(found_Parameters[1]);
     cout << "Available CPU cores: " << this->CPU_cores << endl

diff --git a/cancer_Host.cu b/cancer_Host.cu
diff --git a/cancer_Host.cuh b/cancer_Host.cuh
@@ -167,7 +167,7 @@ public:
 
     void simulate_cell_Round(functions_library &functions, string &multi_Read, int &num_Cuda_devices, int *CUDA_device_IDs,
                              int &num_of_Cells, int &start, int &stop,
-                             int *parents_in_Tissue, int &tissue, string tissue_Name,
+                             vector<int> &parents_in_Tissue, int &tissue, string tissue_Name,
                              vector<pair<int, int>> &indexed_Tissue_Folder,
                              string this_Gen_intermediary_Sequences,
                              int &overall_Generations,
@@ -215,11 +215,11 @@ public:
     //                                    int &start, int &stop, int cell_Count,
     //                                    int *CUDA_device_IDs);
 
-    string find_Sequences_Master(int &offset, int &tissue, string &tissue_Name, functions_library &functions, string &folder_Path, int *parents_in_Tissue, int &num_Sequences, vector<pair<int, int>> &indexed_Tissue_Folder, int &current_Generation, vector<int> &parent_IDs, float *parents_Elapsed, int &last_index_Seq_Written, mt19937 &gen,
+    string find_Sequences_Master(int &offset, int &tissue, string &tissue_Name, functions_library &functions, string &folder_Path, vector<int> &parents_in_Tissue, int &num_Sequences, vector<pair<int, int>> &indexed_Tissue_Folder, int &current_Generation, vector<int> &parent_IDs, float *parents_Elapsed, int &last_index_Seq_Written, mt19937 &gen,
                                  int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List,
                                  string &viral_Migration);
 
-    void thread_find_Files(int offset, int start, int stop, int *parents_in_Tissue, vector<pair<int, int>> &indexed_Tissue_Folder);
+    void thread_find_Files(int offset, int start, int stop, vector<int> &parents_in_Tissue, vector<pair<int, int>> &indexed_Tissue_Folder);
 
     void thread_Sequence_to_String_Cancer(int start, int stop, int **progeny_Sequences);
 

diff --git a/main b/main
diff --git a/parameters_Cancer/individual_Profiles/all_Profiles/profile_1.json b/parameters_Cancer/individual_Profiles/all_Profiles/profile_1.json
@@ -4,7 +4,7 @@
   "Terminal load distribution type":"Fixed",
   "Terminal load Binomial trials":100000,
   "Terminal load Binomial probability":"0.75",
-  "Terminal load Fixed":1000,
+  "Terminal load Fixed":100000,
 
   "Tissue profiles":{
 

diff --git a/parameters_Cancer/parameters_MASTER.json b/parameters_Cancer/parameters_MASTER.json
@@ -23,7 +23,7 @@
   "Stop after generations":"Yes",
   # Generations or Date can be used to stop the simulation as well
   "Mode to stop":"Generations",
-  "Number of generations":5,
+  "Number of generations":20,
   "End date":"2024-01-12",
 
   # Node profile parameter file location

diff --git a/parameters_Cancer/sequence_Profiles/sequence_Master.json b/parameters_Cancer/sequence_Profiles/sequence_Master.json
@@ -35,11 +35,11 @@
 
     "Number of regions":5,
 
-    "Region 1":"100_100",
-    "Region 2":"50_200",
-    "Region 3":"10_10",
-    "Region 4":"1_100",
-    "Region 5":"200_300",
+    "Region 1":"1_10",
+    "Region 2":"20_100",
+    "Region 3":"15_50",
+    "Region 4":"50_75",
+    "Region 5":"80_90",
 
   },
 
@@ -49,7 +49,7 @@
 
     "Hotspot 1":{
 
-      "Region":"100_100",
+      "Region":"1_100",
       # Clock model, can follow a Poisson or Negative Binomial distribution or be Fixed.
       "Clock model":"Poisson",
 
@@ -81,7 +81,7 @@
 
     "Hotspot 2":{
 
-      "Region":"10000_20000",
+      "Region":"50_50",
       # Clock model, can follow a Poisson or Negative Binomial distribution or be Fixed.
       "Clock model":"Negative Binomial",