Enable spectification of thread number

src/Newickform.c

@@ -162,15 +162,15 @@ int max_distance_to_tips(newick_node *root) {
     return max_distance;
 }
 
-newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns,int length_of_original_genome,int min_snps, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag)
+newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns,int length_of_original_genome,int min_snps, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int num_threads)
 {
 	int iLen, iMaxLen;
 	char *pcTreeStr;
 	char *pcInputFile;
 	char *pcOutputFile;
 	char acStrArray[256];
 	newick_node *root;
-    char *returnchar;
+  char *returnchar;
 
 	FILE *f;
 
@@ -249,7 +249,6 @@ newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp
   }
 
   // Initiate multithreading
-  int num_threads = 1; // Adjust as needed
   pthread_t threads[num_threads];
   struct ThreadData threadData[num_threads];
 

src/Newickform.h

@@ -77,12 +77,12 @@ struct ThreadData {
 
 #ifdef __NEWICKFORM_C__
 newick_node* parseTree(char *str);
-newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns,  int length_of_original_genome,int min_snps, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag);
+newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns,  int length_of_original_genome,int min_snps, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int num_threads);
 void print_tree(newick_node *root, FILE * outputfile);
 char* strip_quotes(char *taxon);
 #else
 extern newick_node* parseTree(char *str);
-extern newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome,int min_snps, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag);
+extern newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome,int min_snps, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int num_threads);
 void* threadFunction(void* arg);
 extern void print_tree(newick_node *root, FILE * outputfile);
 void fill_nodeArray(newick_node *root, newick_node** nodeArray);

src/gubbins.c

@@ -39,16 +39,16 @@
 // given a sample name extract the sequences from the vcf
 // compare two sequences to get pseudo sequnece and fill in with difference from reference sequence
 
-void run_gubbins(char vcf_filename[], char tree_filename[],char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag)
+void run_gubbins(char vcf_filename[], char tree_filename[],char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int num_threads)
 {
 	load_sequences_from_multifasta_file(multi_fasta_filename);
-	extract_sequences(vcf_filename, tree_filename, multi_fasta_filename,min_snps,original_multi_fasta_filename,window_min, window_max, uncorrected_p_value, trimming_ratio, extensive_search_flag);
+	extract_sequences(vcf_filename, tree_filename, multi_fasta_filename,min_snps,original_multi_fasta_filename,window_min, window_max, uncorrected_p_value, trimming_ratio, extensive_search_flag, num_threads);
 	create_tree_statistics_file(tree_filename,get_sample_statistics(),number_of_samples_from_parse_phylip());
 	freeup_memory();
 }
 
 
-void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fasta_filename[],int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag)
+void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fasta_filename[],int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int num_threads)
 {
 	FILE *vcf_file_pointer;
 	vcf_file_pointer=fopen(vcf_filename, "r");
@@ -74,7 +74,7 @@ void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fast
 
 	get_integers_from_column_in_vcf(vcf_file_pointer, snp_locations, number_of_snps, column_number_for_column_name(column_names, "POS", number_of_columns));
 
-	root_node = build_newick_tree(tree_filename, vcf_file_pointer,snp_locations, number_of_snps, column_names, number_of_columns, length_of_original_genome,min_snps,window_min, window_max, uncorrected_p_value, trimming_ratio, extensive_search_flag);
+	root_node = build_newick_tree(tree_filename, vcf_file_pointer,snp_locations, number_of_snps, column_names, number_of_columns, length_of_original_genome,min_snps,window_min, window_max, uncorrected_p_value, trimming_ratio, extensive_search_flag, num_threads);
 	fclose(vcf_file_pointer);
 
 	int* filtered_snp_locations = calloc((number_of_snps+1), sizeof(int));

src/gubbins.h

@@ -23,8 +23,8 @@
 #include "seqUtil.h"
 #include "Newickform.h"
 
-void run_gubbins(char vcf_filename[], char tree_filename[], char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag);
-void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag);
+void run_gubbins(char vcf_filename[], char tree_filename[], char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int num_threads);
+void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fasta_filename[], int min_snps, char original_multi_fasta_filename[], int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int n_threads);
 char find_first_real_base(int base_position,  int number_of_child_sequences, char ** child_sequences);
 
 

src/main.c

@@ -86,6 +86,7 @@ int main (int argc, char ** argv)
     float uncorrected_p_value = 0.05;
     float trimming_ratio = 1.0;
     int extensive_search_flag = 0;
+    int num_threads = 1;
     program_name = argv[0];
 
     while (1)
@@ -103,6 +104,7 @@ int main (int argc, char ** argv)
             {"p_value",             required_argument, 0, 'p'},
             {"trimming_ratio",      required_argument, 0, 'i'},
             {"extended_search",     required_argument, 0, 'x'},
+            {"ncpu",                required_argument, 0, 'n'},
 
             {0, 0, 0, 0}
         };
@@ -157,6 +159,9 @@ int main (int argc, char ** argv)
             case 't':
                 memcpy(tree_filename, optarg, size_of_string(optarg) +1);
                 break;
+            case 'n':
+                num_threads = atoi(optarg);
+                break;
             case '?':
                 /* getopt_long already printed an error message. */
                 break;
@@ -188,7 +193,8 @@ int main (int argc, char ** argv)
                     window_max,
                     uncorrected_p_value,
                     trimming_ratio,
-                    extensive_search_flag);
+                    extensive_search_flag,
+                    num_threads);
     }
     else
     {