/* This file is part of Jellyfish.
Jellyfish is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Jellyfish is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Jellyfish. If not, see .
*/
#include
#include
#include
#include
#include
#include
#include
#include
#include
namespace {
using jellyfish::mer_dna;
static const size_t nb_inserts = 10000;
static const double error_rate = 0.001;
template
class MerDnaBloomTest : public ::testing::Test { };
struct TestBloomCounter {
typedef jellyfish::mer_dna_bloom_counter bloom_type;
typedef jellyfish::mer_dna_bloom_counter_file file_type;
static const unsigned int threshold_twice = 2; // Bloom counter counts up to 2.
};
struct TestBloomFilter {
typedef jellyfish::mer_dna_bloom_filter bloom_type;
typedef jellyfish::mer_dna_bloom_filter_file file_type;
static const unsigned int threshold_twice = 1; // Bloom filter counts up to 1.
};
typedef ::testing::Types TestBloomCounterTypes;
TYPED_TEST_CASE(MerDnaBloomTest, TestBloomCounterTypes);
TYPED_TEST(MerDnaBloomTest, FalsePositive) {
mer_dna::k(50);
std::set mer_set;
typename TypeParam::bloom_type bc(error_rate, nb_inserts);
size_t collisions2 = 0;
size_t collisions3 = 0;
// Insert once nb_inserts. Insert twice the first half
{
// First insertion
size_t nb_collisions = 0;
mer_dna m;
for(size_t i = 0; i < nb_inserts; ++i) {
m.randomize();
mer_set.insert(m);
nb_collisions += bc.insert(m) > 0;
}
// EXPECT_GT(error_rate * nb_inserts, nb_collisions);
if(error_rate * nb_inserts < nb_collisions)
std::cerr << "First insertion high error rate: " << nb_collisions << " > "
<< (error_rate * nb_inserts) << '\n';
}
// Second insertion
{
size_t nb_collisions = 0;
size_t nb_errors = 0;
auto it = mer_set.cbegin();
for(size_t i =0; i < nb_inserts / 2; ++i, ++it) {
unsigned int oc = bc.insert(*it);
nb_collisions += oc > 1;
nb_errors += oc < 1;
}
EXPECT_EQ((size_t)0, nb_errors);
// EXPECT_GT(2 * error_rate * nb_inserts, nb_collisions);
if(2 * error_rate * nb_inserts < nb_collisions)
std::cerr << "Second insertion high error rate: " << nb_collisions << " > "
<< (2 * error_rate * nb_inserts) << '\n';
}
// Write to file and reload two different ways
file_unlink f("bloom_file");
{
std::ofstream out(f.path.c_str());
bc.write_bits(out);
EXPECT_TRUE(out.good());
EXPECT_EQ(bc.nb_bytes(), out.tellp());
}
std::ifstream in(f.path.c_str());
typename TypeParam::bloom_type bc_read(bc.m(), bc.k(), in, bc.hash_functions());
EXPECT_EQ(bc.nb_bytes(), in.tellg());
in.close();
typename TypeParam::file_type bc_map(bc.m(), bc.k(), f.path.c_str(), bc.hash_functions());
EXPECT_EQ(bc.m(), bc_read.m());
EXPECT_EQ(bc.k(), bc_read.k());
EXPECT_EQ(bc.m(), bc_map.m());
EXPECT_EQ(bc.k(), bc_map.k());
// Check known mers
{
size_t nb_collisions = 0;
size_t nb_errors = 0;
auto it = mer_set.cbegin();
for(size_t i = 0; i < nb_inserts; ++i, ++it) {
unsigned int check = bc.check(*it);
EXPECT_EQ(check, bc_read.check(*it));
EXPECT_EQ(check, bc_map.check(*it));
if(i < nb_inserts / 2) {
nb_errors += check < TypeParam::threshold_twice;
} else {
nb_errors += check < 1;
nb_collisions += check > 1;
}
}
EXPECT_EQ((size_t)0, nb_errors);
// EXPECT_GT(2 * error_rate * nb_inserts, nb_collisions);
if(2 * error_rate * nb_inserts < nb_collisions)
std::cerr << "Check known mers high error rate: " << nb_collisions << " > "
<< (2 * error_rate * nb_inserts) << '\n';
}
// Check unknown mers
{
size_t nb_collisions = 0;
mer_dna m;
for(size_t i = 0; i < nb_inserts; ++i) {
m.randomize();
unsigned int check = bc.check(m);
EXPECT_EQ(check, bc_read.check(m));
EXPECT_EQ(check, bc_map.check(m));
nb_collisions += check > 0;
}
// EXPECT_GT(2 * error_rate * nb_inserts, nb_collisions);
if(2 * error_rate * nb_inserts < nb_collisions)
std::cerr << "Check unknown mers high error rate: " << nb_collisions << " > "
<< (2 * error_rate * nb_inserts) << '\n';
}
}
TYPED_TEST(MerDnaBloomTest, Move) {
mer_dna::k(100);
typename TypeParam::bloom_type bc(error_rate, nb_inserts);
const unsigned long k = bc.k();
const size_t m = bc.m();
typename TypeParam::bloom_type bc2(std::move(bc));
EXPECT_EQ(k, bc2.k());
EXPECT_EQ(m, bc.m());
}
}