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@nickjcroucher
nickjcroucher committed Apr 19, 2024
1 parent 3df6875 commit b6e75ac
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292 changes: 146 additions & 146 deletions src/branch_sequences.c
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Original file line number Diff line number Diff line change
Expand Up @@ -302,152 +302,152 @@ void carry_unambiguous_gaps_up_tree(newick_node *root)
}
}

void generate_branch_sequences(newick_node *node, char * node_sequences, char * node_names, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome, int num_stored_nodes, 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;

char * node_sequence = (char *) calloc((number_of_snps +1),sizeof(char));

if (node->childNum == 0)
{

get_sequence_for_sample_name(node_sequence, node->taxon);

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(node_sequence, 0,number_of_snps, length_of_original_genome);
set_genome_length_without_gaps_for_sample(node->taxon,branch_genome_size);

}
else
{
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 sequence

while (child != NULL)
{
// Retrieve child sequences from store
for (int seq_store_index = 0; seq_store_index < num_stored_nodes; ++seq_store_index)
{
if (node_names[seq_store_index] == *child->node->taxon) {
child_sequences[child_counter] = &node_sequences[seq_store_index];
break;
}
}
child_nodes[child_counter] = child->node;

// Remove from store as cannot be children of any other nodes
// TO DO

char delimiter_string[3] = {" "};
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.

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(node_sequence, node->taxon);

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< (node->childNum); current_branch++)
{
int * branches_snp_sites;
branches_snp_sites = (int *) calloc((number_of_snps +1),sizeof(int));
char * branch_snp_sequence;
char * branch_snp_ancestor_sequence;
branch_snp_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
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(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,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,
branches_snp_sites,
branch_genome_size,
number_of_branch_snps,
snp_locations,
child_nodes[current_branch],
block_file_pointer,
node,
branch_snp_sequence,
gff_file_pointer,
min_snps,
length_of_original_genome,
node_sequence,
window_min,
window_max,
uncorrected_p_value,
trimming_ratio,
extensive_search_flag);
free(branch_snp_sequence);
free(branch_snp_ancestor_sequence);
free(branches_snp_sites);

}

// Store node sequence
for (int seq_store_index = 0; seq_store_index < num_stored_nodes; ++seq_store_index)
{
if (node_names[seq_store_index] == ' ') {
node_names[seq_store_index] = *node->taxon;
node_sequences[seq_store_index] = *node_sequence;
break;
}
}

}
}


// Windows need to be of a fixed size
// calculate window size
// starting at coord of first snp, count number of snps which fall into window
// if region is blank, move on
int calculate_window_size(int branch_genome_size, int number_of_branch_snps,int window_min, int window_max, int min_snps, int window_factor)
{
int window_size = 0;
if(number_of_branch_snps == 0)
{
return window_min;
}

window_size = (int) ((branch_genome_size*1.0)/(window_factor*number_of_branch_snps*1.0/(min_snps - 1)));

if(window_size < window_min)
{
return window_min;
}
else if(window_size > window_max)
{
return window_max;
}

return window_size;
}
//void generate_branch_sequences(newick_node *node, char * node_sequences, char * node_names, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome, int num_stored_nodes, 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;
//
// char * node_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
//
// if (node->childNum == 0)
// {
//
// get_sequence_for_sample_name(node_sequence, node->taxon);
//
// 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(node_sequence, 0,number_of_snps, length_of_original_genome);
// set_genome_length_without_gaps_for_sample(node->taxon,branch_genome_size);
//
// }
// else
// {
// 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 sequence
//
// while (child != NULL)
// {
// // Retrieve child sequences from store
// for (int seq_store_index = 0; seq_store_index < num_stored_nodes; ++seq_store_index)
// {
// if (node_names[seq_store_index] == *child->node->taxon) {
// child_sequences[child_counter] = &node_sequences[seq_store_index];
// break;
// }
// }
// child_nodes[child_counter] = child->node;
//
// // Remove from store as cannot be children of any other nodes
// // TO DO
//
// char delimiter_string[3] = {" "};
// 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.
//
// 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(node_sequence, node->taxon);
//
// 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< (node->childNum); current_branch++)
// {
// int * branches_snp_sites;
// branches_snp_sites = (int *) calloc((number_of_snps +1),sizeof(int));
// char * branch_snp_sequence;
// char * branch_snp_ancestor_sequence;
// branch_snp_sequence = (char *) calloc((number_of_snps +1),sizeof(char));
// 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(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,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,
// branches_snp_sites,
// branch_genome_size,
// number_of_branch_snps,
// snp_locations,
// child_nodes[current_branch],
// block_file_pointer,
// node,
// branch_snp_sequence,
// gff_file_pointer,
// min_snps,
// length_of_original_genome,
// node_sequence,
// window_min,
// window_max,
// uncorrected_p_value,
// trimming_ratio,
// extensive_search_flag);
// free(branch_snp_sequence);
// free(branch_snp_ancestor_sequence);
// free(branches_snp_sites);
//
// }
//
// // Store node sequence
// for (int seq_store_index = 0; seq_store_index < num_stored_nodes; ++seq_store_index)
// {
// if (node_names[seq_store_index] == ' ') {
// node_names[seq_store_index] = *node->taxon;
// node_sequences[seq_store_index] = *node_sequence;
// break;
// }
// }
//
// }
//}
//
//
//// Windows need to be of a fixed size
//// calculate window size
//// starting at coord of first snp, count number of snps which fall into window
//// if region is blank, move on
//int calculate_window_size(int branch_genome_size, int number_of_branch_snps,int window_min, int window_max, int min_snps, int window_factor)
//{
// int window_size = 0;
// if(number_of_branch_snps == 0)
// {
// return window_min;
// }
//
// window_size = (int) ((branch_genome_size*1.0)/(window_factor*number_of_branch_snps*1.0/(min_snps - 1)));
//
// if(window_size < window_min)
// {
// return window_min;
// }
// else if(window_size > window_max)
// {
// return window_max;
// }
//
// return window_size;
//}


void get_likelihood_for_windows(char * child_sequence, int current_num_snps, int * snp_site_coords, int branch_genome_size, int number_of_branch_snps, int * snp_locations, newick_node * current_node, FILE * block_file_pointer, newick_node *root, char * branch_snp_sequence, FILE * gff_file_pointer, int min_snps, int length_of_original_genome, char * original_sequence,int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag)
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2 changes: 1 addition & 1 deletion src/branch_sequences.h
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
#define _BRANCH_SEQUENCES_H_
#include "seqUtil.h"
#include "Newickform.h"
void generate_branch_sequences(newick_node *root, char * node_sequences, char * node_names, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome, int num_stored_nodes, 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);
//void generate_branch_sequences(newick_node *root, char * node_sequences, char * node_names, FILE *vcf_file_pointer,int * snp_locations, int number_of_snps, char** column_names, int number_of_columns, int length_of_original_genome, int num_stored_nodes, 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);
void identify_recombinations(int number_of_branch_snps, int * branches_snp_sites,int length_of_original_genome);
double calculate_snp_density(int * branches_snp_sites, int number_of_branch_snps, int index);
void get_likelihood_for_windows(char * child_sequence, int current_num_snps, int * snp_site_coords, int branch_genome_size, int number_of_branch_snps, int * snp_locations, newick_node * current_node, FILE * block_file_pointer, newick_node *root, char * branch_snp_sequence, FILE * gff_file_pointer,int min_snps, int length_of_original_genome, char * original_sequence,int window_min, int window_max, float uncorrected_p_value, float trimming_ratio, int extensive_search_flag);
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