Changes to formatting

src/Newickform.c

@@ -191,26 +191,26 @@ newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp
  root = parseTree(pcTreeStr);
 
  // output tab file
-  FILE * block_file_pointer;
-  char block_file_name[MAX_FILENAME_SIZE] = {""};
-  char block_file_extension[5]= {".tab"};
+ FILE * block_file_pointer;
+ char block_file_name[MAX_FILENAME_SIZE] = {""};
+ char block_file_extension[5]= {".tab"};
  memcpy(block_file_name, filename, size_of_string(filename) +1);
  concat_strings_created_with_malloc(block_file_name,block_file_extension);
  block_file_pointer = fopen(block_file_name, "w");
 
  // output tab file
-  FILE * branch_snps_file_pointer;
-  char branch_snps_file_name[MAX_FILENAME_SIZE]= {""};
-  char branchtab_extension[18]= {".branch_snps.tab"};
+ FILE * branch_snps_file_pointer;
+ char branch_snps_file_name[MAX_FILENAME_SIZE]= {""};
+ char branchtab_extension[18]= {".branch_snps.tab"};
  memcpy(branch_snps_file_name, filename, size_of_string(filename) +1);
  concat_strings_created_with_malloc(branch_snps_file_name,branchtab_extension);
  branch_snps_file_pointer = fopen(branch_snps_file_name, "w");
 
  // output gff file
  FILE * gff_file_pointer;
-  char gff_file_name[MAX_FILENAME_SIZE]= {""};
-  memcpy(gff_file_name, filename, size_of_string(filename) +1);
-  char gff_extension[5]= {".gff"};
+ char gff_file_name[MAX_FILENAME_SIZE]= {""};
+ memcpy(gff_file_name, filename, size_of_string(filename) +1);
+ char gff_extension[5]= {".gff"};
  concat_strings_created_with_malloc(gff_file_name,gff_extension);
  gff_file_pointer = fopen(gff_file_name, "w");
  print_gff_header(gff_file_pointer,length_of_original_genome);
@@ -307,25 +307,6 @@ newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp
 
  }
 
-// char * root_sequence = NULL;
-// root_sequence = generate_branch_sequences(root,
-// vcf_file_pointer,
-// snp_locations,
-// number_of_snps,
-// column_names,
-// number_of_columns,
-// root_sequence,
-// length_of_original_genome,
-// block_file_pointer,
-// gff_file_pointer,
-// min_snps,
-// branch_snps_file_pointer,
-// window_min,
-// window_max,
-// uncorrected_p_value,
-// trimming_ratio,
-// extensive_search_flag);
-// free(root_sequence);
  free(nodeArray);
  free(node_depths);
  free(node_sequences);