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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 <cstring>
#include <seqan3/std/filesystem>
#include <fstream>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/io/sequence_file/output.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/performance/units.hpp>
#include <seqan3/test/seqan2.hpp>
#include <seqan3/test/tmp_filename.hpp>
#if SEQAN3_HAS_SEQAN2
#include <seqan/seq_io.h>
#endif // SEQAN3_HAS_SEQAN2
constexpr unsigned default_seed = 1234u;
// ============================================================================
// generate fastq file
// ============================================================================
inline constexpr size_t default_sequence_length = 50; //length of nucleotide and quality sequence
inline std::string const fastq_id{"the fastq file"};
std::string generate_fastq_string(size_t const entries_size)
{
std::ostringstream stream_buffer{};
seqan3::sequence_file_output fastq_ostream{stream_buffer, seqan3::format_fastq{}};
auto seed = default_seed;
for (size_t i = 0; i < entries_size; ++i, ++seed)
{
auto random_sequence = seqan3::test::generate_sequence<seqan3::dna5>(default_sequence_length, 0, seed);
auto random_qualities = seqan3::test::generate_sequence<seqan3::phred42>(default_sequence_length, 0, seed);
fastq_ostream.emplace_back(random_sequence, fastq_id, random_qualities);
}
stream_buffer.flush();
return stream_buffer.str();
}
// ============================================================================
// save file on disc temporarily
// ============================================================================
auto create_fastq_file_for(std::string const & fastq_string)
{
// create temporary file, automatically removed on destruction
seqan3::test::tmp_filename fastq_file{"format_fastq_benchmark_test_file.fastq"};
auto fastq_file_path = fastq_file.get_path();
// fill temporary file with a fastq file
std::ofstream ostream{fastq_file_path};
ostream << fastq_string;
ostream.close();
return fastq_file;
}
// ============================================================================
// seqan3 fastq output benchmark
// ============================================================================
// ----------------------------------------------------------------------------
// write dummy fastq file to a string stream
// ----------------------------------------------------------------------------
void fastq_write_to_stream_seqan3(benchmark::State & state)
{
size_t const iterations_per_run = state.range(0);
std::ostringstream ostream;
seqan3::sequence_file_output fout{ostream, seqan3::format_fastq{}, seqan3::fields<seqan3::field::id,
seqan3::field::seq,
seqan3::field::qual>{}};
auto seq = seqan3::test::generate_sequence<seqan3::dna5>(default_sequence_length, 0, default_seed);
auto qual = seqan3::test::generate_sequence<seqan3::phred42>(default_sequence_length, 0, default_seed);
for (auto _ : state)
{
for (size_t i = 0; i < iterations_per_run; ++i)
fout.emplace_back(fastq_id, seq, qual);
}
ostream.str(""); // Reset stream.
fout.emplace_back(fastq_id, seq, qual); // Write one entry.
ostream.flush(); // Make sure the buffer is flushed.
size_t bytes_per_run = ostream.str().size() * iterations_per_run;
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
BENCHMARK(fastq_write_to_stream_seqan3)->Arg(100)->Arg(1000)->Arg(10000);
// ============================================================================
// seqan3 fastq input benchmark
// ============================================================================
// ----------------------------------------------------------------------------
// read dummy fastq file from a stream
// ----------------------------------------------------------------------------
void fastq_read_from_stream_seqan3(benchmark::State & state)
{
size_t const iterations_per_run = state.range(0);
std::string fastq_file = generate_fastq_string(iterations_per_run);
std::istringstream istream{fastq_file};
seqan3::sequence_file_input fastq_file_in{istream, seqan3::format_fastq{}};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = fastq_file_in.begin();
for (size_t i = 0; i < iterations_per_run; ++i)
it++;
}
size_t bytes_per_run = fastq_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
// ----------------------------------------------------------------------------
// read dummy fastq file from temporary file on disk
// ----------------------------------------------------------------------------
void fastq_read_from_disk_seqan3(benchmark::State & state)
{
size_t const iterations_per_run = state.range(0);
std::string fastq_file = generate_fastq_string(iterations_per_run);
auto file_name = create_fastq_file_for(fastq_file);
for (auto _ : state)
{
seqan3::sequence_file_input fastq_file_in{file_name.get_path()};
auto it = fastq_file_in.begin();
for (size_t i = 0; i < iterations_per_run; ++i)
it++;
}
size_t bytes_per_run = fastq_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
// ============================================================================
// seqan2 fastq input benchmark
// ============================================================================
#if SEQAN3_HAS_SEQAN2
// ----------------------------------------------------------------------------
// read dummy fastq file from a stream
// ----------------------------------------------------------------------------
void fastq_read_from_stream_seqan2(benchmark::State & state)
{
size_t const iterations_per_run = state.range(0);
std::string fastq_file = generate_fastq_string(iterations_per_run);
std::istringstream istream{fastq_file};
seqan::CharString id{};
seqan::Dna5String seq{};
seqan::CharString qual{};
for (auto _ : state)
{
istream.clear();
istream.seekg(0, std::ios::beg);
auto it = seqan::Iter<std::istringstream, seqan::StreamIterator<seqan::Input> >(istream);
for (size_t i = 0; i < iterations_per_run; ++i)
{
readRecord(id, seq, qual, it, seqan::Fastq{});
clear(id);
clear(seq);
clear(qual);
}
}
size_t bytes_per_run = fastq_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
// ----------------------------------------------------------------------------
// read dummy fastq file from temporary file on disk
// ----------------------------------------------------------------------------
void fastq_read_from_disk_seqan2(benchmark::State & state)
{
size_t const iterations_per_run = state.range(0);
std::string fastq_file = generate_fastq_string(iterations_per_run);
auto file_name = create_fastq_file_for(fastq_file);
seqan::CharString id{};
seqan::Dna5String seq{};
seqan::CharString qual{};
for (auto _ : state)
{
seqan::SeqFileIn seqFileIn(file_name.get_path().c_str());
auto it = seqFileIn.iter;
for (size_t i = 0; i < iterations_per_run; ++i)
{
readRecord(id, seq, qual, it, seqan::Fastq{});
clear(id);
clear(seq);
clear(qual);
}
}
size_t bytes_per_run = fastq_file.size();
state.counters["iterations_per_run"] = iterations_per_run;
state.counters["bytes_per_run"] = bytes_per_run;
state.counters["bytes_per_second"] = seqan3::test::bytes_per_second(bytes_per_run);
}
#endif // SEQAN3_HAS_SEQAN2
BENCHMARK(fastq_read_from_stream_seqan3)->Arg(100)->Arg(1000)->Arg(10000);
BENCHMARK(fastq_read_from_disk_seqan3)->Arg(100)->Arg(1000)->Arg(10000);
#if SEQAN3_HAS_SEQAN2
BENCHMARK(fastq_read_from_stream_seqan2)->Arg(100)->Arg(1000)->Arg(10000);
BENCHMARK(fastq_read_from_disk_seqan2)->Arg(100)->Arg(1000)->Arg(10000);
#endif // SEQAN3_HAS_SEQAN2
BENCHMARK_MAIN();
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