void Debloom_check1 ()
{
size_t kmerSize = 11;
size_t miniSize = 8;
size_t nks = 1;
const char* seqs[] = {
"CGCTACAGCAGCTAGTTCATCATTGTTTATCAATGATAAAATATAATAAGCTAAAAGGAAACTATAAATA"
"ACCATGTATAATTATAAGTAGGTACCTATTTTTTTATTTTAAACTGAAATTCAATATTATATAGGCAAAG"
} ;
/** We configure parameters for a SortingCountAlgorithm object. */
IProperties* params = SortingCountAlgorithm<>::getDefaultProperties(); LOCAL (params);
params->setInt (STR_KMER_SIZE, kmerSize);
params->setInt (STR_MINIMIZER_SIZE, miniSize);
params->setInt (STR_MAX_MEMORY, MAX_MEMORY);
params->setInt (STR_KMER_ABUNDANCE_MIN, nks);
params->setStr (STR_URI_OUTPUT, "foo");
/** We create a SortingCountAlgorithm object. */
SortingCountAlgorithm<> sortingCount (new BankStrings (seqs, ARRAY_SIZE(seqs)), params);
/** We launch DSK. */
sortingCount.execute();
CPPUNIT_ASSERT (sortingCount.getSolidCounts()->getNbItems() == (int64_t)(strlen(seqs[0]) - kmerSize + 1) );
/** We get the storage instance. */
Storage* storage = sortingCount.getStorage();
LOCAL (storage);
Partition<SortingCountAlgorithm<>::Count>& counts = storage->getGroup("dsk").getPartition<Kmer<>::Count> ("solid");
/** We create a bloom instance. */
float nbitsPerKmer = DebloomAlgorithm<>::getNbBitsPerKmer (kmerSize, DEBLOOM_ORIGINAL);
BloomAlgorithm<> bloom (*storage, &counts, kmerSize, nbitsPerKmer, 0, BLOOM_BASIC);
bloom.execute ();
/** We create a debloom instance. */
DebloomAlgorithm<> debloom (
storage->getGroup("bloom"),
storage->getGroup("debloom"),
&counts, kmerSize, miniSize, 1000, 0, BLOOM_BASIC, DEBLOOM_ORIGINAL
);
/** We launch the debloom. */
debloom.execute();
/** The following values have been computed with the original minia. */
u_int64_t values[] =
{
0xc0620, 0x288f40, 0x188f40, 0x2aaa29, 0x8000b, 0x200881, 0x288081, 0x820db, 0x52e23, 0x2888f,
0xaaa8b, 0x28838d, 0x20000, 0xa93ab, 0x2c18d, 0x2ba89, 0x183600, 0xea00b, 0x1a4ea0, 0xf8585
};
set<Kmer<>::Type> okValues;
for (unsigned int i = 0; i < ARRAY_SIZE(values); i++)
{
Kmer<>::Type val; val.setVal(values[i]);
okValues.insert(val);
}
CPPUNIT_ASSERT (debloom.getCriticalKmers()->getNbItems() == ARRAY_SIZE(values));
/** We iterate the cFP kmers. */
set<Kmer<>::Type> checkValues;
Iterator<Kmer<>::Type>* iter = debloom.getCriticalKmers()->iterator();
LOCAL (iter);
for (iter->first(); !iter->isDone(); iter->next())
{
set<Kmer<>::Type>::iterator lookup = okValues.find (iter->item());
CPPUNIT_ASSERT (lookup != okValues.end());
checkValues.insert (iter->item());
}
CPPUNIT_ASSERT (checkValues.size() == okValues.size());
}
