From 5478d658918c6a260bdc6e68cd15be812c3c198b Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Tue, 23 Apr 2024 09:45:22 +0100 Subject: [PATCH] Remove obsolete function --- src/Newickform.c | 3 --- src/branch_sequences.c | 24 ------------------------ 2 files changed, 27 deletions(-) diff --git a/src/Newickform.c b/src/Newickform.c index 97f5eb79..e5ff9a28 100644 --- a/src/Newickform.c +++ b/src/Newickform.c @@ -252,9 +252,6 @@ newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp int num_threads = 1; // Adjust as needed pthread_t threads[num_threads]; struct ThreadData threadData[num_threads]; - - // First carry gaps up tree - carry_unambiguous_gaps_up_tree(root); // iterate through depths and identify batches of analyses to be run for (int depth = 0; depth <= max_depth; ++depth) diff --git a/src/branch_sequences.c b/src/branch_sequences.c index f8f2b445..a7b7d804 100644 --- a/src/branch_sequences.c +++ b/src/branch_sequences.c @@ -279,30 +279,6 @@ int calculate_number_of_bases_in_recombations_excluding_gaps(int ** block_coordi return total_bases; } -void carry_unambiguous_gaps_up_tree(newick_node *root) -{ - if(root->childNum > 0) - { - newick_child *child; - int parent_sequence_index = find_sequence_index_from_sample_name(root->taxon); - - child = root->child; - int child_sequence_indices[root->childNum]; - int child_counter = 0; - while (child != NULL) - { - child_sequence_indices[child_counter] = find_sequence_index_from_sample_name(child->node->taxon); - carry_unambiguous_gaps_up_tree(child->node); - child = child->next; - child_counter++; - } - - // compare the parent sequence to the each child sequence and update the gaps - fill_in_unambiguous_gaps_in_parent_from_children(parent_sequence_index, child_sequence_indices,child_counter); - //fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap(parent_sequence_index, child_sequence_indices,child_counter); - } -} - void generate_branch_sequences(newick_node *node, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome, FILE * block_file_pointer, FILE * gff_file_pointer,int min_snps,FILE * branch_snps_file_pointer, int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag, int thread_index) { newick_child *child;