void get_coverage_on_panels(int* percentage_coverage,int* median_coverage,
StrBuf** panel_file_paths,
int max_branch_len, dBGraph *db_graph,
int ignore_first, int ignore_last , int NUM_PANELS)
{
int i;
FILE* fp;
AlleleInfo* ai = alloc_allele_info();
int number_of_reads = 0;
int number_of_covered_reads =0;
int num_kmers=0;
Covg tot_pos_kmers;
Covg tot_kmers;
Covg med;
//----------------------------------
// allocate the memory used to read the sequences
//----------------------------------
Sequence * seq = malloc(sizeof(Sequence));
if (seq == NULL)
{
die("Out of memory trying to allocate Sequence");
}
alloc_sequence(seq,max_branch_len,LINE_MAX);
//We are going to load all the bases into a single sliding window
KmerSlidingWindow* kmer_window = malloc(sizeof(KmerSlidingWindow));
if (kmer_window==NULL)
{
die("Failed to malloc kmer sliding window");
}
CovgArray* working_ca = alloc_and_init_covg_array(max_branch_len);
dBNode** array_nodes = (dBNode**) malloc(sizeof(dBNode*)*max_branch_len);
Orientation* array_or =(Orientation*) malloc(sizeof(Orientation)*max_branch_len);
kmer_window->kmer = (BinaryKmer*) malloc(sizeof(BinaryKmer)*(max_branch_len-db_graph->kmer_size+1));
if (kmer_window->kmer==NULL)
{
die("Failed to malloc kmer_window->kmer");
}
kmer_window->nkmers=0;
//create file readers
int file_reader_fasta(FILE * fp, Sequence * seq, int max_read_length, boolean new_entry, boolean * full_entry)
{
long long ret;
int offset = 0;
if (new_entry == false)
{
offset = db_graph->kmer_size;
}
ret = read_sequence_from_fasta(fp,seq,max_read_length,new_entry,full_entry,offset);
return ret;
}
void test_get_next_gene_info()
{
uint16_t kmer_size = 31;
int number_of_bits = 10;
int bucket_size = 100;
int max_retries = 10;
dBGraph *db_graph= hash_table_new(number_of_bits, bucket_size,
max_retries, kmer_size);
int max_gene_len = 1500;
uint64_t* kmer_covg_array = calloc(150, sizeof(uint64_t));
uint64_t* readlen_array = calloc(max_gene_len, sizeof(uint64_t));
StrBuf* list = strbuf_create("../data/test/myKrobe/predictor/gene_presence/sample1.fa.list");
unsigned long long num_bases = build_unclean_graph(db_graph,
list, true,
kmer_size,
readlen_array, max_gene_len,
kmer_covg_array, 150,
false, 0);
FILE* fp = fopen("../data/test/myKrobe/predictor/gene_presence/panel1.fasta", "r");
if (fp==NULL)
{
die("Cannot open this file: ../data/test/myKrobe/predictor/gene_presence/panel1.fasta");
}
GeneInfo* gi = alloc_and_init_gene_info();
//----------------------------------
// allocate the memory used to read the sequences
//----------------------------------
Sequence * seq = malloc(sizeof(Sequence));
if (seq == NULL){
die("Out of memory trying to allocate Sequence");
}
alloc_sequence(seq,max_gene_len,LINE_MAX);
//We are going to load all the bases into a single sliding window
KmerSlidingWindow* kmer_window = malloc(sizeof(KmerSlidingWindow));
if (kmer_window==NULL)
{
die("Failed to malloc kmer sliding window");
}
kmer_window->kmer = (BinaryKmer*) malloc(sizeof(BinaryKmer)*(max_gene_len-db_graph->kmer_size+1));
if (kmer_window->kmer==NULL)
{
die("Failed to malloc kmer_window->kmer");
}
kmer_window->nkmers=0;
// int max_gene_len = 5000;
CovgArray* working_ca = alloc_and_init_covg_array(max_gene_len);
//end of intialisation
//create file readers
int file_reader_fasta(FILE * fp, Sequence * seq, int max_read_length, boolean new_entry, boolean * full_entry){
long long ret;
int offset = 0;
if (new_entry == false){
offset = db_graph->kmer_size;
}
ret = read_sequence_from_fasta(fp,seq,max_read_length,new_entry,full_entry,offset);
return ret;
}
