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Rename variables to help rewrite
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@nickjcroucher
nickjcroucher committed Apr 19, 2024
1 parent 98a8854 commit 8865558
Showing 1 changed file with 25 additions and 25 deletions.
50 changes: 25 additions & 25 deletions src/branch_sequences.c
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Original file line number Diff line number Diff line change
Expand Up @@ -302,34 +302,34 @@ void carry_unambiguous_gaps_up_tree(newick_node *root)
}
}

char *generate_branch_sequences(newick_node *root, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, char * leaf_sequence, 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)
char *generate_branch_sequences(newick_node *node, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, char * node_sequence, 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)
{
newick_child *child;
int child_counter = 0;
int current_branch =0;
int branch_genome_size = 0;
int number_of_branch_snps=0;

if (root->childNum == 0)
if (node->childNum == 0)
{
leaf_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
get_sequence_for_sample_name(leaf_sequence, root->taxon);
node_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
get_sequence_for_sample_name(node_sequence, node->taxon);

root->taxon_names = (char *) calloc(MAX_SAMPLE_NAME_SIZE,sizeof(char));
memcpy(root->taxon_names, root->taxon, size_of_string(root->taxon)+1);
node->taxon_names = (char *) calloc(MAX_SAMPLE_NAME_SIZE,sizeof(char));
memcpy(node->taxon_names, node->taxon, size_of_string(node->taxon)+1);

// Save some statistics about the sequence
branch_genome_size = calculate_size_of_genome_without_gaps(leaf_sequence, 0,number_of_snps, length_of_original_genome);
set_genome_length_without_gaps_for_sample(root->taxon,branch_genome_size);
branch_genome_size = calculate_size_of_genome_without_gaps(node_sequence, 0,number_of_snps, length_of_original_genome);
set_genome_length_without_gaps_for_sample(node->taxon,branch_genome_size);

return leaf_sequence;
return node_sequence;
}
else
{
child = root->child;
char * child_sequences[root->childNum];
newick_node * child_nodes[root->childNum];
root->taxon_names = (char *) calloc(MAX_SAMPLE_NAME_SIZE*number_of_columns,sizeof(char));
child = node->child;
char * child_sequences[node->childNum];
newick_node * child_nodes[node->childNum];
node->taxon_names = (char *) calloc(MAX_SAMPLE_NAME_SIZE*number_of_columns,sizeof(char));

// generate pointers for each child seuqn

Expand All @@ -356,25 +356,25 @@ char *generate_branch_sequences(newick_node *root, FILE *vcf_file_pointer,int *
child_nodes[child_counter] = child->node;

char delimiter_string[3] = {" "};
concat_strings_created_with_malloc(root->taxon_names, delimiter_string);
concat_strings_created_with_malloc(root->taxon_names, child_nodes[child_counter]->taxon_names);
concat_strings_created_with_malloc(node->taxon_names, delimiter_string);
concat_strings_created_with_malloc(node->taxon_names, child_nodes[child_counter]->taxon_names);

child_counter++;
child = child->next;
}

// For all bases update the parent sequence with N if all child sequences.

leaf_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
node_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
// All child sequneces should be available use them to find the ancestor sequence
get_sequence_for_sample_name(leaf_sequence, root->taxon);
get_sequence_for_sample_name(node_sequence, node->taxon);

branch_genome_size = calculate_size_of_genome_without_gaps(leaf_sequence, 0,number_of_snps, length_of_original_genome);
set_genome_length_without_gaps_for_sample(root->taxon,branch_genome_size);
branch_genome_size = calculate_size_of_genome_without_gaps(node_sequence, 0,number_of_snps, length_of_original_genome);
set_genome_length_without_gaps_for_sample(node->taxon,branch_genome_size);



for(current_branch = 0 ; current_branch< (root->childNum); current_branch++)
for(current_branch = 0 ; current_branch< (node->childNum); current_branch++)
{
int * branches_snp_sites;
branches_snp_sites = (int *) calloc((number_of_snps +1),sizeof(int));
Expand All @@ -384,11 +384,11 @@ char *generate_branch_sequences(newick_node *root, FILE *vcf_file_pointer,int *
branch_snp_ancestor_sequence = (char *) calloc((number_of_snps +1),sizeof(char));

branch_genome_size = calculate_size_of_genome_without_gaps(child_sequences[current_branch], 0,number_of_snps, length_of_original_genome);
number_of_branch_snps = calculate_number_of_snps_excluding_gaps(leaf_sequence, child_sequences[current_branch], number_of_snps, branches_snp_sites, snp_locations,branch_snp_sequence,branch_snp_ancestor_sequence);
number_of_branch_snps = calculate_number_of_snps_excluding_gaps(node_sequence, child_sequences[current_branch], number_of_snps, branches_snp_sites, snp_locations,branch_snp_sequence,branch_snp_ancestor_sequence);


child_nodes[current_branch]->number_of_snps = number_of_branch_snps;
print_branch_snp_details(branch_snps_file_pointer, child_nodes[current_branch]->taxon,root->taxon, branches_snp_sites, number_of_branch_snps, branch_snp_sequence, branch_snp_ancestor_sequence,child_nodes[current_branch]->taxon_names);
print_branch_snp_details(branch_snps_file_pointer, child_nodes[current_branch]->taxon,node->taxon, branches_snp_sites, number_of_branch_snps, branch_snp_sequence, branch_snp_ancestor_sequence,child_nodes[current_branch]->taxon_names);

get_likelihood_for_windows(child_sequences[current_branch],
number_of_snps,
Expand All @@ -398,12 +398,12 @@ char *generate_branch_sequences(newick_node *root, FILE *vcf_file_pointer,int *
snp_locations,
child_nodes[current_branch],
block_file_pointer,
root,
node,
branch_snp_sequence,
gff_file_pointer,
min_snps,
length_of_original_genome,
leaf_sequence,
node_sequence,
window_min,
window_max,
uncorrected_p_value,
Expand All @@ -416,7 +416,7 @@ char *generate_branch_sequences(newick_node *root, FILE *vcf_file_pointer,int *

}

return leaf_sequence;
return node_sequence;
}
}

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