Merge pull request #227 from puethe/segfault

dynamically allocate memory to avoid stack overflow

VERSION

@@ -1 +1 @@
-2.3.3
+2.3.4

src/gubbins.c

@@ -71,22 +71,22 @@ void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fast
 
  number_of_snps = number_of_snps_in_phylip();
 
- int snp_locations[number_of_snps];
+ int* snp_locations = calloc(number_of_snps, sizeof(int));
 
  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);
  fclose(vcf_file_pointer);
 
- int filtered_snp_locations[number_of_snps];
+ int* filtered_snp_locations = calloc(number_of_snps, sizeof(int));
  int number_of_filtered_snps;
  int number_of_samples = number_of_samples_from_parse_phylip();
 
  char * sample_names[number_of_samples];
- get_sample_names_from_parse_phylip(sample_names);
+  get_sample_names_from_parse_phylip(sample_names);
 
- char * reference_sequence_bases;
- reference_sequence_bases = (char *) calloc((number_of_snps+1),sizeof(char));
+  char * reference_sequence_bases;
+  reference_sequence_bases = (char *) calloc((number_of_snps+1),sizeof(char));
 
  get_sequence_for_sample_name(reference_sequence_bases, sample_names[0]);
  int internal_nodes[number_of_samples];
@@ -97,7 +97,7 @@ void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fast
  }
 
  number_of_filtered_snps = refilter_existing_snps(reference_sequence_bases, number_of_snps, snp_locations, filtered_snp_locations,internal_nodes);
- char * filtered_bases_for_snps[number_of_filtered_snps];
+ char ** filtered_bases_for_snps = (char **) calloc(number_of_filtered_snps, sizeof(char *));
 
  filter_sequence_bases_and_rotate(reference_sequence_bases, filtered_bases_for_snps, number_of_filtered_snps);