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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <benchmark/benchmark.h>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/range/views/kmer_hash.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/performance/naive_kmer_hash.hpp>
#include <seqan3/test/performance/units.hpp>
#ifdef SEQAN3_HAS_SEQAN2
#include <seqan/index.h>
#endif // SEQAN3_HAS_SEQAN2
inline benchmark::Counter bp_per_second(size_t const basepairs)
{
return benchmark::Counter(basepairs,
benchmark::Counter::kIsIterationInvariantRate,
benchmark::Counter::OneK::kIs1000);
}
inline seqan3::shape make_gapped_shape(size_t const k)
{
seqan3::shape shape{};
for (size_t i{0}; i < k - 1; ++i)
shape.push_back((i + 1) % 2);
shape.push_back(1u);
shape.push_back(0u);
return shape;
}
static void arguments(benchmark::internal::Benchmark* b)
{
for (int32_t sequence_length : {1'000, 50'000, /*1'000'000*/})
{
for (int32_t k : {8, /*16, 24,*/ 30})
{
b->Args({sequence_length, k});
}
}
}
static void seqan_kmer_hash_ungapped(benchmark::State & state)
{
auto sequence_length = state.range(0);
assert(sequence_length > 0);
size_t k = static_cast<size_t>(state.range(1));
assert(k > 0);
auto seq = seqan3::test::generate_sequence<seqan3::dna4>(sequence_length, 0, 0);
size_t sum{0};
for (auto _ : state)
{
for (auto h : seq | seqan3::views::kmer_hash(seqan3::ungapped{static_cast<uint8_t>(k)}))
benchmark::DoNotOptimize(sum += h);
}
// prevent complete optimisation
[[maybe_unused]] volatile auto fin = sum;
state.counters["Throughput[bp/s]"] = bp_per_second(sequence_length - k + 1);
}
static void seqan_kmer_hash_gapped(benchmark::State & state)
{
auto sequence_length = state.range(0);
assert(sequence_length > 0);
size_t k = static_cast<size_t>(state.range(1));
assert(k > 0);
auto seq = seqan3::test::generate_sequence<seqan3::dna4>(sequence_length, 0, 0);
size_t sum{0};
for (auto _ : state)
{
for (auto h : seq | seqan3::views::kmer_hash(make_gapped_shape(k)))
benchmark::DoNotOptimize(sum += h);
}
// prevent complete optimisation
[[maybe_unused]] volatile auto fin = sum;
state.counters["Throughput[bp/s]"] = bp_per_second(sequence_length - k + 1);
}
static void naive_kmer_hash(benchmark::State & state)
{
auto sequence_length = state.range(0);
assert(sequence_length > 0);
size_t k = static_cast<size_t>(state.range(1));
assert(k > 0);
auto seq = seqan3::test::generate_sequence<seqan3::dna4>(sequence_length, 0, 0);
size_t sum{0};
for (auto _ : state)
{
for (auto h : seq | seqan3::views::naive_kmer_hash(k))
benchmark::DoNotOptimize(sum += h);
}
// prevent complete optimisation
[[maybe_unused]] volatile auto fin = sum;
state.counters["Throughput[bp/s]"] = bp_per_second(sequence_length - k + 1);
}
#ifdef SEQAN3_HAS_SEQAN2
inline auto make_gapped_shape_seqan2(size_t const k)
{
seqan::String<char> bitmap;
for (size_t i{0}; i < k - 1; ++i)
seqan::append(bitmap, seqan::CharString(std::to_string((i + 1) % 2)));
seqan::append(bitmap, seqan::CharString("1"));
seqan::Shape<seqan::Dna, seqan::GenericShape> s(bitmap);
return s;
}
static void seqan2_kmer_hash_ungapped(benchmark::State & state)
{
auto sequence_length = state.range(0);
assert(sequence_length > 0);
size_t k = static_cast<size_t>(state.range(1));
assert(k > 0);
auto seq = seqan3::test::generate_sequence_seqan2<seqan::Dna>(sequence_length, 0, 0);
seqan::Shape<seqan::Dna, seqan::SimpleShape> s;
seqan::resize(s, k);
size_t sum{0};
for (auto _ : state)
{
auto it = seqan::begin(seq);
seqan::hashInit(s, it);
for (size_t i{0}; i < seqan::length(seq) - k + 1; ++i, ++it)
{
benchmark::DoNotOptimize(sum += seqan::hashNext(s, it));
}
}
// prevent complete optimisation
[[maybe_unused]] volatile auto fin = sum;
state.counters["Throughput[bp/s]"] = bp_per_second(sequence_length - k + 1);
}
static void seqan2_kmer_hash_gapped(benchmark::State & state)
{
auto sequence_length = state.range(0);
assert(sequence_length > 0);
size_t k = static_cast<size_t>(state.range(1));
assert(k > 0);
auto seq = seqan3::test::generate_sequence_seqan2<seqan::Dna>(sequence_length, 0, 0);
seqan::Shape<seqan::Dna, seqan::GenericShape> s = make_gapped_shape_seqan2(k);
size_t sum{0};
for (auto _ : state)
{
auto it = seqan::begin(seq);
seqan::hashInit(s, it);
for (size_t i{0}; i < seqan::length(seq) - k + 1; ++i, ++it)
{
benchmark::DoNotOptimize(sum += seqan::hashNext(s, it));
}
}
// prevent complete optimisation
[[maybe_unused]] volatile auto fin = sum;
state.counters["Throughput[bp/s]"] = bp_per_second(sequence_length - k + 1);
}
BENCHMARK(seqan2_kmer_hash_ungapped)->Apply(arguments);
BENCHMARK(seqan2_kmer_hash_gapped)->Apply(arguments);
#endif // SEQAN3_HAS_SEQAN2
BENCHMARK(seqan_kmer_hash_ungapped)->Apply(arguments);
BENCHMARK(seqan_kmer_hash_gapped)->Apply(arguments);
BENCHMARK(naive_kmer_hash)->Apply(arguments);
BENCHMARK_MAIN();
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