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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 <iostream>
#include <memory>
#include <sstream>
#include <seqan3/io/stream/iterator.hpp>
#ifdef SEQAN3_HAS_ZLIB
#include <seqan3/contrib/stream/bgzf_istream.hpp>
#include <seqan3/contrib/stream/bgzf_ostream.hpp>
#include <seqan3/contrib/stream/gz_istream.hpp>
#include <seqan3/contrib/stream/gz_ostream.hpp>
#endif
// only benchmark BZIP2 if explicitly requested, because slow setup
#if !defined(SEQAN3_BENCH_BZIP2) && defined(SEQAN3_HAS_BZIP2)
#undef SEQAN3_HAS_BZIP2
#endif
#ifdef SEQAN3_HAS_BZIP2
#include <seqan3/contrib/stream/bz2_istream.hpp>
#include <seqan3/contrib/stream/bz2_ostream.hpp>
#endif
// SEQAN2
#if __has_include(<seqan/stream.h>)
#define SEQAN3_HAS_SEQAN2 1
#ifdef SEQAN3_HAS_ZLIB
#define SEQAN_HAS_ZLIB 1
#endif
#ifdef SEQAN3_HAS_BZIP2
#define SEQAN_HAS_BZIP2 1
#endif
#include <seqan/stream.h>
#endif
std::string input
{
[] ()
{
std::string line{"The quick brown fox jumps over the lazy dog"};
std::string ret;
for (size_t i = 0; i < 10'000'000; ++i)
ret += line;
return ret;
} ()
};
template <typename t>
std::string const input_comp;
#ifdef SEQAN3_HAS_SEQAN2
template <>
std::string const & input_comp<seqan::Nothing> = input;
#endif
#ifdef SEQAN3_HAS_ZLIB
template <>
std::string const input_comp<seqan3::contrib::gz_istream>
{
[] ()
{
std::ostringstream ret;
{ // In scope to force flush of ostream on destruction.
seqan3::contrib::gz_ostream os{ret};
std::copy(input.begin(), input.end(), std::ostreambuf_iterator<char>(os));
}
return ret.str();
} ()
};
template <>
std::string const input_comp<seqan3::contrib::bgzf_istream>
{
[] ()
{
std::ostringstream ret;
{ // In scope to force flush of ostream on destruction.
seqan3::contrib::bgzf_ostream os{ret};
std::copy(input.begin(), input.end(), std::ostreambuf_iterator<char>(os));
}
return ret.str();
} ()
};
#ifdef SEQAN3_HAS_SEQAN2
template <>
std::string const & input_comp<seqan::GZFile> = input_comp<seqan3::contrib::gz_istream>;
template <>
std::string const & input_comp<seqan::BgzfFile> = input_comp<seqan3::contrib::bgzf_istream>;
#endif
#endif
#ifdef SEQAN3_HAS_BZIP2
template <>
std::string const input_comp<seqan3::contrib::bz2_istream>
{
[] ()
{
std::ostringstream ret;
{ // In scope to force flush of ostream on destruction.
seqan3::contrib::bz2_ostream os{ret};
std::copy(input.begin(), input.end(), std::ostreambuf_iterator<char>(os));
}
return ret.str();
} ()
};
#ifdef SEQAN3_HAS_SEQAN2
template <>
std::string const & input_comp<seqan::BZ2File> = input_comp<seqan3::contrib::bz2_istream>;
#endif
#endif
// ============================================================================
// plain benchmark of ostringstream
// ============================================================================
void uncompressed(benchmark::State & state)
{
std::istringstream s{input};
size_t i = 0;
for (auto _ : state)
{
s.clear();
s.seekg(0, std::ios::beg);
seqan3::detail::fast_istreambuf_iterator<char> it{*s.rdbuf()};
for (; it != std::default_sentinel; ++it)
i += *it;
}
state.counters["iterations_per_run"] = i;
}
BENCHMARK(uncompressed);
// ============================================================================
// compression applied
// ============================================================================
template <typename compressed_istream_t>
void compressed(benchmark::State & state)
{
std::istringstream s{input_comp<compressed_istream_t>};
size_t i = 0;
for (auto _ : state)
{
s.clear();
s.seekg(0, std::ios::beg);
compressed_istream_t comp{s};
seqan3::detail::fast_istreambuf_iterator<char> it{*comp.rdbuf()};
for (size_t v = 0; v < input_comp<compressed_istream_t>.size(); ++v)
{
i += *it;
++it;
}
}
state.counters["iterations_per_run"] = i;
}
#ifdef SEQAN3_HAS_ZLIB
BENCHMARK_TEMPLATE(compressed, seqan3::contrib::gz_istream);
BENCHMARK_TEMPLATE(compressed, seqan3::contrib::bgzf_istream);
#endif
#ifdef SEQAN3_HAS_BZIP2
BENCHMARK_TEMPLATE(compressed, seqan3::contrib::bz2_istream);
#endif
// ============================================================================
// compression applied, but stuffed into plain istream
// ============================================================================
template <typename compressed_istream_t>
void compressed_type_erased(benchmark::State & state)
{
std::istringstream s{input_comp<compressed_istream_t>};
size_t i = 0;
for (auto _ : state)
{
s.clear();
s.seekg(0, std::ios::beg);
std::unique_ptr<std::istream> comp{new compressed_istream_t{s}};
seqan3::detail::fast_istreambuf_iterator<char> it{*comp->rdbuf()};
for (size_t v = 0; v < input_comp<compressed_istream_t>.size(); ++v)
{
i += *it;
++it;
}
}
state.counters["iterations_per_run"] = i;
}
#ifdef SEQAN3_HAS_ZLIB
BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::gz_istream);
BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::bgzf_istream);
#endif
#ifdef SEQAN3_HAS_BZIP2
BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::bz2_istream);
#endif
// ============================================================================
// compression applied, but stuffed into plain istream, also stringstream erased
// ============================================================================
template <typename compressed_istream_t>
void compressed_type_erased2(benchmark::State & state)
{
std::unique_ptr<std::istream> s{new std::istringstream{input_comp<compressed_istream_t>}};
size_t i = 0;
for (auto _ : state)
{
s->clear();
s->seekg(0, std::ios::beg);
std::unique_ptr<std::istream> comp{new compressed_istream_t{*s}};
seqan3::detail::fast_istreambuf_iterator<char> it{*comp->rdbuf()};
for (size_t v = 0; v < input_comp<compressed_istream_t>.size(); ++v)
{
i += *it;
++it;
}
}
state.counters["iterations_per_run"] = i;
}
#ifdef SEQAN3_HAS_ZLIB
BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::gz_istream);
BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::bgzf_istream);
#endif
#ifdef SEQAN3_HAS_BZIP2
BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::bz2_istream);
#endif
// ============================================================================
// seqan2 virtual stream
// ============================================================================
#ifdef SEQAN3_HAS_SEQAN2
void seqan2_uncompressed(benchmark::State & state)
{
std::istringstream s{input};
size_t i = 0;
for (auto _ : state)
{
s.clear();
s.seekg(0, std::ios::beg);
auto it = seqan::Iter<std::istringstream, seqan::StreamIterator<seqan::Input> >(s);
for (size_t v = 0; v < input.size(); ++v)
{
i += *it;
++it;
}
}
state.counters["iterations_per_run"] = i;
}
template <typename compression_t, typename stream_t>
void seqan2_compressed_impl(benchmark::State & state)
{
std::istringstream s{input_comp<compression_t>};
size_t i = 0;
for (auto _ : state)
{
s.clear();
s.seekg(0, std::ios::beg);
stream_t comp{s};
auto it = seqan::Iter<std::istringstream, seqan::StreamIterator<seqan::Input> >(comp);
for (size_t v = 0; v < input_comp<compression_t>.size(); ++v)
{
i += *it;
++it;
}
}
state.counters["iterations_per_run"] = i;
}
template <typename compression_type>
void seqan2_compressed(benchmark::State & state)
{
#ifdef SEQAN_HAS_ZLIB
if constexpr (std::is_same_v<compression_type, seqan::GZFile>)
seqan2_compressed_impl<seqan::GZFile, zlib_stream::zip_istream>(state);
else if constexpr (std::is_same_v<compression_type, seqan::BgzfFile>)
seqan2_compressed_impl<seqan::BgzfFile, seqan::bgzf_istream>(state);
#endif // SEQAN_HAS_ZLIB
#ifdef SEQAN_HAS_BZIP2
if constexpr (std::is_same_v<compression_type, seqan::BZ2File>)
seqan2_compressed_impl<seqan::BZ2File, bzip2_stream::bzip2_istream>(state);
#endif // SEQAN_HAS_BZIP2
if constexpr (std::is_same_v<compression_type, seqan::Nothing>)
seqan2_uncompressed(state);
}
BENCHMARK_TEMPLATE(seqan2_compressed, seqan::Nothing);
#ifdef SEQAN_HAS_ZLIB
BENCHMARK_TEMPLATE(seqan2_compressed, seqan::GZFile);
BENCHMARK_TEMPLATE(seqan2_compressed, seqan::BgzfFile);
#endif
#ifdef SEQAN_HAS_BZIP2
BENCHMARK_TEMPLATE(seqan2_compressed, seqan::BZ2File);
#endif
#endif // SEQAN3_HAS_SEQAN2
// ============================================================================
// instantiate tests
// ============================================================================
BENCHMARK_MAIN();
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