cp_hashtable* associate_samples_and_positions(vcf_file_t* file) {
LOG_DEBUG_F("** %zu sample names read\n", file->samples_names->size);
array_list_t *sample_names = file->samples_names;
cp_hashtable *sample_ids = cp_hashtable_create(sample_names->size * 2,
cp_hash_string,
(cp_compare_fn) strcasecmp
);
int *index;
char *name;
for (int i = 0; i < sample_names->size; i++) {
name = sample_names->items[i];
index = (int*) malloc (sizeof(int)); *index = i;
if (cp_hashtable_get(sample_ids, name)) {
LOG_FATAL_F("Sample %s appears more than once. File can not be analyzed.\n", name);
}
cp_hashtable_put(sample_ids, name, index);
}
// char **keys = (char**) cp_hashtable_get_keys(sample_ids);
// int num_keys = cp_hashtable_count(sample_ids);
// for (int i = 0; i < num_keys; i++) {
// printf("%s\t%d\n", keys[i], *((int*) cp_hashtable_get(sample_ids, keys[i])));
// }
return sample_ids;
}
cp_hashtable *load_hasthable_codes() {
cp_hashtable *t = cp_hashtable_create(400,
cp_hash_istring,
(cp_compare_fn)strcasecmp);
/*const unsigned char COMBINATORIAL = (NUCLEOTIDES_NUM * NUCLEOTIDES_NUM * NUCLEOTIDES_NUM) + (NUCLEOTIDES_NUM * NUCLEOTIDES_NUM) + NUCLEOTIDES_NUM;
unsigned char *id_array = (unsigned char *)malloc(sizeof(unsigned char)*COMBINATORIAL);
*/
size_t id = 0;
char combination[4];
combination[3] = '\0';
for(unsigned int nt_1 = 0; nt_1 < NUCLEOTIDES_NUM; nt_1++){
combination[0] = NUCLEOTIDES[nt_1];
for(unsigned int nt_2 = 0; nt_2 < NUCLEOTIDES_NUM; nt_2++){
combination[1] = NUCLEOTIDES[nt_2];
for(unsigned int nt_3 = 0; nt_3 < NUCLEOTIDES_NUM; nt_3++){
combination[2] = NUCLEOTIDES[nt_3];
cp_hashtable_put(t, strdup(combination), (void *)id);
id++;
}
}
}
// printf("Table size %d\n", t->table_size);
combination[2] = '\0';
for(unsigned int nt_1 = 0; nt_1 < NUCLEOTIDES_NUM; nt_1++){
combination[0] = NUCLEOTIDES[nt_1];
for(unsigned int nt_2 = 0; nt_2 < NUCLEOTIDES_NUM; nt_2++){
combination[1] = NUCLEOTIDES[nt_2];
cp_hashtable_put(t, strdup(combination), (void *)id);
id++;
}
}
//printf("Table size %d\n", t->table_size);
combination[1] = '\0';
for(unsigned int nt = 0; nt < NUCLEOTIDES_NUM; nt++){
combination[0] = NUCLEOTIDES[nt];
cp_hashtable_put(t, strdup(combination), (void *)id);
id++;
}
return t;
}
int main(int argc, char *argv[])
{
int i;
cp_thread w[COUNT];
cp_thread r[COUNT];
long total;
int rc;
if (argc > 1) silent = atoi(argv[1]);
for (i = 0; i < COUNT; i++)
{
rc = cp_mutex_init(&lock[i], NULL);
cp_cond_init(&cond[i], NULL);
t[i] = cp_hashtable_create(10, cp_hash_string, cp_hash_compare_string);
tl[i] = cp_list_create();
}
rc = cp_mutex_init(&start_mutex, NULL);
cp_cond_init(&start_cond, NULL);
for (i = 0; i < COUNT; i++)
cp_thread_create(r[i], NULL, reader, (void *) i);
for (i = 0; i < COUNT; i++)
cp_thread_create(w[i], NULL, writer, (void *) INSERTS);
printf("press enter\n");
getchar();
cp_mutex_lock(&start_mutex);
running = 1;
total = time(NULL);
cp_cond_broadcast(&start_cond);
rc = cp_mutex_unlock(&start_mutex);
if (rc == 0) write_err("MAIN");
for (i = 0; i < COUNT; i++)
cp_thread_join(w[i], NULL);
running = 0;
for (i = 0; i < COUNT; i++)
{
cp_mutex_lock(&lock[i]);
cp_cond_broadcast(&cond[i]);
cp_mutex_unlock(&lock[i]);
cp_thread_join(r[i], NULL);
}
total = time(NULL) - total;
printf("\ndone in %ld seconds. tables should be empty now. press enter.\n",
total);
getchar();
for (i = 0; i < COUNT; i++)
{
printf("table %d: %ld items\n", i, cp_hashtable_count(t[i]));
cp_hashtable_destroy(t[i]);
printf("list %d: %ld items\n", i, cp_list_item_count(tl[i]));
while (cp_list_item_count(tl[i]))
{
char *leftover = cp_list_remove_head(tl[i]);
printf(" * %s\n", leftover);
}
cp_list_destroy(tl[i]);
}
printf("deleted them tables. press enter.\n");
getchar();
printf("bye.\n");
return 0;
}