boolean element_is_key(Key key, Element e, short kmer_size)
{
if (key == NULL) {
printf("Do not call element_is_key wth a NULL pointer. Exiting\n");
exit(1);
}
return binary_kmer_comparison_operator(*key, e.kmer);
}
Orientation db_node_get_orientation(BinaryKmer * k, Element * e, short kmer_size)
{
if (binary_kmer_comparison_operator(e->kmer, *k) == true) {
return forward;
}
BinaryKmer tmp_kmer;
if (binary_kmer_comparison_operator(e->kmer,
*(binary_kmer_reverse_complement
(k, kmer_size,
&tmp_kmer))) == true) {
return reverse;
}
printf("programming error - you have called db_node_get_orientation with a kmer that is neither equal to the kmer in this node, nor its rev comp\n");
char tmpseq1[kmer_size];
char tmpseq2[kmer_size];
printf("Arg 1 Kmer is %s and Arg 2 node kmer is %s\n",
binary_kmer_to_seq(k, kmer_size, tmpseq1),
binary_kmer_to_seq(&(e->kmer), kmer_size, tmpseq2));
exit(1);
}
void test_hash_table_find_or_insert()
{
short kmer_size;
long long max_key_given_kmer_size;
//adds binary kmers to a hash, then tries to find them
//will go through all possible bin kmers given the kmer_size, stepping
// with granulatiry step. Since for kmer_size large (eg 21) it takes to long to try ALL
// possible 21-mers, the last argument allows you to specify the largest one to test
BinaryKmer tmp_kmer;
BinaryKmer tmp_kmer2;
void test(short kmer_size, int num_bits, int bucket, int max_tries, int step, long long max_kmer_to_test)
{
int number_of_bits = num_bits;
int bucket_size = bucket;
long long bad_reads = 0;
int max_retries = max_tries;
boolean found = false;
HashTable* hash_table = hash_table_new(number_of_bits,bucket_size,max_retries,kmer_size);
long long i;
for (i=0; i< max_kmer_to_test; i++)
{
BinaryKmer b;
binary_kmer_initialise_to_zero(&b);
b[NUMBER_OF_BITFIELDS_IN_BINARY_KMER-1]=(bitfield_of_64bits) i;
hash_table_find_or_insert(element_get_key(&b, hash_table->kmer_size, &tmp_kmer),&found, hash_table);
if (found==false)
{
CU_ASSERT(binary_kmer_comparison_operator(b,*(element_get_key(&b, hash_table->kmer_size, &tmp_kmer)) ) );
}
}
Element* e=NULL;
for (i=0; i< max_kmer_to_test; i=i+step)
{
BinaryKmer b;
binary_kmer_initialise_to_zero(&b);
b[NUMBER_OF_BITFIELDS_IN_BINARY_KMER-1]=(bitfield_of_64bits) i;
e = hash_table_find(element_get_key(&b,hash_table->kmer_size,&tmp_kmer), hash_table);
CU_ASSERT(e!=NULL);
if (e !=NULL)
{
CU_ASSERT(binary_kmer_comparison_operator(e->kmer, *element_get_key(&b, hash_table->kmer_size, &tmp_kmer2)) );
}
else
{
die("Error: e is NULL for i=%lld - unable to find\n",i);
}
}
hash_table_free(&hash_table);
CU_ASSERT(hash_table == NULL);
}
