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[TEST] Adapt tests
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@eseiler
eseiler committed Oct 11, 2023
1 parent c0408ba commit bc00548
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39 changes: 10 additions & 29 deletions test/unit/hibf/sketch/estimate_kmer_counts_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

#include <cinttypes> // for uint8_t
#include <cstddef> // for size_t
#include <random> // for uniform_int_distribution, mt19937_64
#include <string> // for basic_string, string
#include <string_view> // for string_view
#include <vector> // for allocator, vector
Expand All @@ -11,40 +12,20 @@

TEST(estimate_kmer_counts_test, small_example)
{
std::vector<std::string> const input_sequences{
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"},
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"ATATCGATCGAGCGAGGCAGGCAGCGATCGAGCGAGCGCATGCAGCGACTAGCTACGACAGCTACTATCAGCAGCGAGCG"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"},
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"ATCGATCACGATCAGCGAGCGATATCTTATCGTAGGCATCGAGCATCGAGGAGCGATCTATCTATCTATCATCTATCTAT"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"
"G"}};

uint8_t const kmer_size{19};
size_t const b = 12;
seqan::hibf::sketch::hyperloglog sketch(b);

for (std::string_view const seq : input_sequences)
for (size_t pos = 0; pos + kmer_size <= seq.size(); ++pos) // substr is [pos, pos + len)
sketch.add(seq.substr(pos, kmer_size));
seqan::hibf::sketch::hyperloglog sketch(12);

std::uniform_int_distribution<uint64_t> distribution{};
std::mt19937_64 engine{0u};

for (size_t i = 0; i < 1500; ++i)
sketch.add(distribution(engine));

std::vector<seqan::hibf::sketch::hyperloglog> sketches{sketch, sketch};
std::vector<size_t> kmer_counts;

seqan::hibf::sketch::estimate_kmer_counts(sketches, kmer_counts);

ASSERT_EQ(kmer_counts.size(), 2);
EXPECT_EQ(kmer_counts[0], 581);
EXPECT_EQ(kmer_counts[1], 581);
EXPECT_EQ(kmer_counts[0], 1498);
EXPECT_EQ(kmer_counts[1], 1498);
}
165 changes: 66 additions & 99 deletions test/unit/hibf/sketch/hyperloglog_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,18 @@
#include <cstddef> // for size_t
#include <filesystem> // for path
#include <fstream> // for ofstream, ifstream, basic_ostream::write, ios
#include <random> // for uniform_int_distribution, mt19937_64
#include <ranges> // for iota_view, operator==, _Iota, iota
#include <stdexcept> // for runtime_error, invalid_argument
#include <string> // for allocator, basic_string, hash, string, char_traits, operator==
#include <string_view> // for string_view
#include <unordered_set> // for unordered_set
#include <vector> // for vector

#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
#include <hibf/test/sandboxed_path.hpp> // for operator/, sandboxed_path
#include <hibf/test/tmp_directory.hpp> // for tmp_directory
#include <hibf/contrib/std/chunk_view.hpp> // for chunk_view, operator==, chunk, chunk_fn
#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
#include <hibf/test/sandboxed_path.hpp> // for operator/, sandboxed_path
#include <hibf/test/tmp_directory.hpp> // for tmp_directory

TEST(hyperloglog, bit_widths)
{
Expand All @@ -40,24 +42,24 @@ TEST(hyperloglog, initialization)

TEST(hyperloglog, add_and_estimate_small)
{
seqan::hibf::sketch::hyperloglog sketch{};

// XXH3_64bits hash -> first 4 bits: 0000, rank: 3
sketch.add("bla");
// XXH3_64bits hash -> first 4 bits: 1011, rank: 2
sketch.add("bli");
// XXH3_64bits hash -> first 4 bits: 0100, rank: 2
sketch.add("blub");
// XXH3_64bits hash -> first 4 bits: 1110, rank: 1
sketch.add("bloink");
// XXH3_64bits hash -> first 4 bits: 0000, rank: 3
sketch.add("blubba");
// XXH3_64bits hash -> first 4 bits: 1101, rank: 1
sketch.add("blumpf");
// XXH3_64bits hash -> first 4 bits: 1001, rank: 2
sketch.add("blarkse");
// XXH3_64bits hash -> first 4 bits: 1000, rank: 2
sketch.add("bladuzel");
seqan::hibf::sketch::hyperloglog sketch{5u};

// first 4 bits of hash: 0000, rank: 3
sketch.add(255881241332063154ULL);
// first 4 bits of hash: 1011, rank: 2
sketch.add(13132817195163223578ULL);
// first 4 bits of hash: 0100, rank: 2
sketch.add(5120631300412165844ULL);
// first 4 bits of hash: 1110, rank: 1
sketch.add(16862690419523416066ULL);
// first 4 bits of hash: 0000, rank: 3
sketch.add(148518882728022940ULL);
// first 4 bits of hash: 1101, rank: 1
sketch.add(15892358469365346306ULL);
// first 4 bits of hash: 1001, rank: 2
sketch.add(10885195586503739779ULL);
// first 4 bits of hash: 1000, rank: 2
sketch.add(9563173945158404745ULL);

// estimate = alpha * m * m / sum(2^(-M_[j]))
// = 0.697 * 32 * 32 / (89/8)
Expand All @@ -74,14 +76,14 @@ TEST(hyperloglog, clear)
// Same as add_and_estimate_small
seqan::hibf::sketch::hyperloglog sketch{};

sketch.add("bla");
sketch.add("bli");
sketch.add("blub");
sketch.add("bloink");
sketch.add("blubba");
sketch.add("blumpf");
sketch.add("blarkse");
sketch.add("bladuzel");
sketch.add(255881241332063154ULL);
sketch.add(13132817195163223578ULL);
sketch.add(5120631300412165844ULL);
sketch.add(16862690419523416066ULL);
sketch.add(148518882728022940ULL);
sketch.add(15892358469365346306ULL);
sketch.add(10885195586503739779ULL);
sketch.add(9563173945158404745ULL);

EXPECT_NEAR(sketch.estimate(), 7.899522493, 0.0000001);

Expand All @@ -90,41 +92,30 @@ TEST(hyperloglog, clear)
EXPECT_EQ(sketch.estimate(), 0.0);
}

std::vector<std::string> const input_sequences{
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"},
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"ATATCGATCGAGCGAGGCAGGCAGCGATCGAGCGAGCGCATGCAGCGACTAGCTACGACAGCTACTATCAGCAGCGAGCG"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"},
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"ATCGATCACGATCAGCGAGCGATATCTTATCGTAGGCATCGAGCATCGAGGAGCGATCTATCTATCTATCATCTATCTAT"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"
"G"}};
std::vector<uint64_t> const input_values = []()
{
auto generator = []()
{
std::uniform_int_distribution<uint64_t> distribution{};
std::mt19937_64 engine{0u};
return distribution(engine);
};

std::vector<uint64_t> result(1500);
std::ranges::generate(result, generator);
return result;
}();

TEST(hyperloglog, add_and_estimate_large)
{
size_t const kmer_size{16u};
seqan::hibf::sketch::hyperloglog sketch{};

std::unordered_set<std::string_view> control;
std::unordered_set<uint64_t> control;

// put every sequence in this file into the sketch
for (std::string_view const seq : input_sequences)
for (uint64_t value : input_values)
{
for (size_t pos = 0; pos + kmer_size <= seq.size(); ++pos) // substr is [pos, pos + len)
{
control.insert(seq.substr(pos, kmer_size));
sketch.add(seq.substr(pos, kmer_size));
}
control.insert(value);
sketch.add(value);
}

// the estimate is greater than 2.5 * 16, therefore this is the raw estimate
Expand All @@ -136,22 +127,14 @@ TEST(hyperloglog, add_and_estimate_small_SIMD)
{
seqan::hibf::sketch::hyperloglog sketch{};

// XXH3_64bits hash -> first 4 bits: 0000, rank: 3
sketch.add("bla");
// XXH3_64bits hash -> first 4 bits: 1011, rank: 2
sketch.add("bli");
// XXH3_64bits hash -> first 4 bits: 0100, rank: 2
sketch.add("blub");
// XXH3_64bits hash -> first 4 bits: 1110, rank: 1
sketch.add("bloink");
// XXH3_64bits hash -> first 4 bits: 0000, rank: 3
sketch.add("blubba");
// XXH3_64bits hash -> first 4 bits: 1101, rank: 1
sketch.add("blumpf");
// XXH3_64bits hash -> first 4 bits: 1001, rank: 2
sketch.add("blarkse");
// XXH3_64bits hash -> first 4 bits: 1000, rank: 2
sketch.add("bladuzel");
sketch.add(255881241332063154ULL);
sketch.add(13132817195163223578ULL);
sketch.add(5120631300412165844ULL);
sketch.add(16862690419523416066ULL);
sketch.add(148518882728022940ULL);
sketch.add(15892358469365346306ULL);
sketch.add(10885195586503739779ULL);
sketch.add(9563173945158404745ULL);

seqan::hibf::sketch::hyperloglog other{sketch};

Expand All @@ -160,24 +143,25 @@ TEST(hyperloglog, add_and_estimate_small_SIMD)

TEST(hyperloglog, merge_and_merge_SIMD)
{
size_t const kmer_size{16u};
size_t const chunks{10u};
size_t const chunk_size{(input_values.size() + chunks - 1u) / chunks};

seqan::hibf::sketch::hyperloglog full_sketch{};
seqan::hibf::sketch::hyperloglog merge_sketch{};
seqan::hibf::sketch::hyperloglog merge_SIMD_sketch{};

std::vector<seqan::hibf::sketch::hyperloglog> partial_sketches;

// put every sequence in this file into the full_sketch
// and add a disjointed sketch for every sequence to partial_sketches
for (std::string_view const seq : input_sequences)
// put every chunk into the full full_sketch
// and add a disjointed sketch for every chunk to partial_sketches
for (auto && chunk : input_values | seqan::stl::views::chunk(chunk_size))
{
partial_sketches.emplace_back();

for (size_t pos = 0; pos + kmer_size <= seq.size(); ++pos) // substr is [pos, pos + len)
for (uint64_t value : chunk)
{
partial_sketches.back().add(seq.substr(pos, kmer_size));
full_sketch.add(seq.substr(pos, kmer_size));
partial_sketches.back().add(value);
full_sketch.add(value);
}
}

Expand Down Expand Up @@ -271,15 +255,11 @@ TEST(hyperloglog, fail_restore_bit_width)

TEST(hyperloglog, dump_and_restore)
{
size_t const kmer_size{16u};

seqan::hibf::sketch::hyperloglog dump_sketch{};
seqan::hibf::sketch::hyperloglog restore_sketch{};

// put every sequence in this file into the dump_sketch
for (std::string_view const seq : input_sequences)
for (size_t pos = 0; pos + kmer_size <= seq.size(); ++pos) // substr is [pos, pos + len)
dump_sketch.add(seq.substr(pos, kmer_size));
for (uint64_t value : input_values)
dump_sketch.add(value);

// create temp file
seqan::hibf::test::tmp_directory tmp_dir{};
Expand All @@ -296,16 +276,3 @@ TEST(hyperloglog, dump_and_restore)
// now dump_sketch and restore_sketch should be equal
EXPECT_EQ(dump_sketch.estimate(), restore_sketch.estimate());
}

TEST(hyperloglog, add_integer)
{
uint64_t const value{87123921398671ULL};

seqan::hibf::sketch::hyperloglog sketch_as_sv{};
sketch_as_sv.add(std::string_view{reinterpret_cast<char const *>(&value), sizeof(uint64_t)});

seqan::hibf::sketch::hyperloglog sketch_as_int{};
sketch_as_int.add(value);

EXPECT_EQ(sketch_as_sv.estimate(), sketch_as_int.estimate());
}
40 changes: 10 additions & 30 deletions test/unit/hibf/sketch/toolbox_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
#include <cstddef> // for size_t
#include <functional> // for greater
#include <limits> // for numeric_limits
#include <random> // for uniform_int_distribution, mt19937_64
#include <string> // for allocator, basic_string, string
#include <string_view> // for string_view
#include <tuple> // for tie, make_tuple
Expand All @@ -24,33 +25,12 @@ struct toolbox_test : public ::testing::Test
{
seqan::hibf::sketch::hyperloglog sketch{};

std::vector<std::string> const small_input{
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"},
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"ATATCGATCGAGCGAGGCAGGCAGCGATCGAGCGAGCGCATGCAGCGACTAGCTACGACAGCTACTATCAGCAGCGAGCG"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"},
{"ACGATCGACTAGGAGCGATTACGACTGACTACATCTAGCTAGCTAGAGATTCTTCAGAGCTTAGCGATCTCGAGCTATCG"
"AGCTATTTCAGACCTACACTATCTAGCTTATTCACAAATATTATAACGGCATACGTCTAGTGCTCATCGTGATCTAGCGA"
"GCTAGCGATCTGATTCACGAGCGTACGTGACGTACGTATCGTACTACGTATCGTACTACATGCATCGATCGACGTAGCTA"
"ATCGATCACGATCAGCGAGCGATATCTTATCGTAGGCATCGAGCATCGAGGAGCGATCTATCTATCTATCATCTATCTAT"
"TCAGCGTAGCGTACGAGTCAGCTGACTGACGTCGTAGCATCGTACGTAGCGTAGCGATCGAGTCACTTATCGTAGCTAGT"
"CGACTAGCGTACGTAGTCAGCTATTATGACGAGGCGACTTAGCGACTACGAGCTAGCGAGGAGGCGAGGCGAGCGGACTG"
"G"}};

size_t const kmer_size{21u};

for (std::string_view const seq : small_input)
for (size_t pos = 0; pos + kmer_size <= seq.size(); ++pos) // substr is [pos, pos + len)
sketch.add(seq.substr(pos, kmer_size));

// seqan::hibf::sketch::toolbox::read_hll_files_into(data(""), test_filenames, result);
std::uniform_int_distribution<uint64_t> distribution{};
std::mt19937_64 engine{0u};

for (size_t i = 0; i < 1500; ++i)
sketch.add(distribution(engine));

return std::vector<seqan::hibf::sketch::hyperloglog>(test_kmer_counts.size(), sketch);
}();
};
Expand Down Expand Up @@ -82,21 +62,21 @@ TEST_F(toolbox_test, precompute_union_estimates_for)
test_kmer_counts,
test_positions,
1);
EXPECT_RANGE_EQ(estimates, (std::vector<uint64_t>{658, 600, 0, 0}));
EXPECT_RANGE_EQ(estimates, (std::vector<uint64_t>{1635, 600, 0, 0}));

seqan::hibf::sketch::toolbox::precompute_union_estimates_for(estimates,
test_sketches,
test_kmer_counts,
test_positions,
2);
EXPECT_RANGE_EQ(estimates, (std::vector<uint64_t>{658, 658, 700, 0}));
EXPECT_RANGE_EQ(estimates, (std::vector<uint64_t>{1635, 1635, 700, 0}));

seqan::hibf::sketch::toolbox::precompute_union_estimates_for(estimates,
test_sketches,
test_kmer_counts,
test_positions,
3);
EXPECT_RANGE_EQ(estimates, (std::vector<uint64_t>{658, 658, 658, 800}));
EXPECT_RANGE_EQ(estimates, (std::vector<uint64_t>{1635, 1635, 1635, 800}));
}

TEST_F(toolbox_test, random_shuffle)
Expand Down

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