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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#include <benchmark/benchmark.h>
#include "global_affine_alignment_simd_benchmark_template.hpp"
// Range to test for sequence length variance
inline constexpr size_t deviation_begin = 0;
inline constexpr size_t deviation_end = 64;
inline constexpr size_t deviation_step = 8;
// ----------------------------------------------------------------------------
// SeqAn3
// ----------------------------------------------------------------------------
constexpr auto nt_score_scheme = seqan3::nucleotide_scoring_scheme{seqan3::match_score{4}, seqan3::mismatch_score{-5}};
constexpr auto affine_cfg =
seqan3::align_cfg::method_global{}
| seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10}, seqan3::align_cfg::extension_score{-1}}
| seqan3::align_cfg::scoring_scheme{nt_score_scheme};
BENCHMARK_CAPTURE(seqan3_affine_accelerated,
simd_with_score,
seqan3::dna4{},
affine_cfg,
seqan3::align_cfg::output_score{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan3_affine_accelerated,
simd_with_end_position,
seqan3::dna4{},
affine_cfg,
seqan3::align_cfg::output_score{},
seqan3::align_cfg::output_end_position{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan3_affine_accelerated,
simd_parallel_with_score,
seqan3::dna4{},
affine_cfg,
seqan3::align_cfg::output_score{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{},
seqan3::align_cfg::parallel{get_number_of_threads()})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan3_affine_accelerated,
simd_parallel_with_end_position,
seqan3::dna4{},
affine_cfg,
seqan3::align_cfg::output_score{},
seqan3::align_cfg::output_end_position{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{},
seqan3::align_cfg::parallel{get_number_of_threads()})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
#ifdef SEQAN3_HAS_SEQAN2
// ----------------------------------------------------------------------------
// SeqAn2
// ----------------------------------------------------------------------------
// Note SeqAn2 has no parallel interface yet for computing the traceback as well.
BENCHMARK_CAPTURE(seqan2_affine_accelerated,
simd_with_score,
seqan2::Dna{},
seqan2::Score<int16_t>{4, -5, -1, -11},
seqan2::ExecutionPolicy<seqan2::Serial, seqan2::Vectorial>{},
1,
affine_cfg)
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan2_affine_accelerated,
simd_parallel_with_score,
seqan2::Dna{},
seqan2::Score<int16_t>{4, -5, -1, -11},
seqan2::ExecutionPolicy<seqan2::Parallel, seqan2::Vectorial>{},
get_number_of_threads(),
affine_cfg)
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
#endif // SEQAN3_HAS_SEQAN2
// ============================================================================
// instantiate tests
// ============================================================================
BENCHMARK_MAIN();
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