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@wvdtoorn
wvdtoorn committed Aug 13, 2020
1 parent 2db85cf commit f86ea7c
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Showing 10 changed files with 36 additions and 31 deletions.
5 changes: 3 additions & 2 deletions test/performance/alignment/global_affine_alignment_benchmark.cpp
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Expand Up @@ -26,11 +26,12 @@
#include <seqan/align.h>
#endif

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{seqan3::gap_scheme{seqan3::gap_score{-1},
seqan3::gap_open_score{-10}}} |
seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}};
seqan3::align_cfg::scoring_scheme{nt_score_scheme};

// ============================================================================
// affine; score; dna4; single
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5 changes: 3 additions & 2 deletions test/performance/alignment/global_affine_alignment_parallel_benchmark.cpp
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Expand Up @@ -31,11 +31,12 @@
#include <seqan/align_parallel.h>
#endif

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{seqan3::gap_scheme{seqan3::gap_score{-1},
seqan3::gap_open_score{-10}}} |
seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}};
seqan3::align_cfg::scoring_scheme{nt_score_scheme};

// Aliases to beautify the benchmark output
using score = seqan3::detail::with_score_type;
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5 changes: 3 additions & 2 deletions test/performance/alignment/global_affine_alignment_simd_benchmark.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,12 @@
#include <seqan/align_parallel.h>
#endif

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{seqan3::gap_scheme{seqan3::gap_score{-1},
seqan3::gap_open_score{-10}}} |
seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}};
seqan3::align_cfg::scoring_scheme{nt_score_scheme};

// Globally defined constants to ensure same test data.
inline constexpr size_t sequence_length = 150;
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5 changes: 3 additions & 2 deletions test/performance/io/format_sam_benchmark.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,10 @@ static std::string create_sam_file_string(size_t const n_queries)
auto reference = seqan3::test::generate_sequence<seqan3::dna4>(reference_size, length_variance, seed);

// align
constexpr auto nt_score_scheme = seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-2}};
auto config = seqan3::align_cfg::method_global{} |
seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-2}}} |
seqan3::align_cfg::scoring_scheme{nt_score_scheme} |
seqan3::align_cfg::gap{seqan3::gap_scheme{seqan3::gap_score{-1}, seqan3::gap_open_score{-10}}} |
seqan3::align_cfg::aligned_ends{seqan3::free_ends_first} |
seqan3::align_cfg::result{seqan3::with_alignment};
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5 changes: 3 additions & 2 deletions test/unit/alignment/pairwise/fixture/global_affine_banded.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,8 @@ namespace seqan3::test::alignment::fixture::global::affine::banded
inline constexpr auto align_config = seqan3::align_cfg::method_global{} |
seqan3::align_cfg::gap{seqan3::gap_scheme{seqan3::gap_score{-1},
seqan3::gap_open_score{-10}}};
inline constexpr auto nt_score_scheme = seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}};

static auto dna4_01 = []()
{ // AACCGGTTAACCGGTT
Expand All @@ -50,8 +52,7 @@ static auto dna4_01 = []()
"ACGTACGTA"_dna4,
align_config | seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-3},
seqan3::align_cfg::upper_diagonal{8}} |
seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::align_cfg::scoring_scheme{nt_score_scheme},
-18,
"A---ACCGGTTAACCGGTT",
"ACGTAC----------GTA",
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12 changes: 6 additions & 6 deletions test/unit/alignment/pairwise/fixture/local_affine_banded.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ static auto dna4_01 = []()
"AACCGGTTTAACCGGTT"_dna4,
"ACGTCTACGTA"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}}
seqan3::mismatch_score{-5}}}
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-2},
seqan3::align_cfg::upper_diagonal{5}},
11,
Expand Down Expand Up @@ -101,7 +101,7 @@ static auto dna4_02 = []()
"ACGTCTACGTA"_dna4,
"AACCGGTTTAACCGGTT"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}}
seqan3::mismatch_score{-5}}}
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-2},
seqan3::align_cfg::upper_diagonal{5}},
8,
Expand Down Expand Up @@ -169,7 +169,7 @@ static auto dna4_03 = []()
seqan3::align_cfg::method_local
| seqan3::align_cfg::gap{seqan3::gap_scheme{seqan3::gap_score{0}, seqan3::gap_open_score{0}}}
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{2},
seqan3::mismatch_score{-1}}}
seqan3::mismatch_score{-1}}}
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{0},
seqan3::align_cfg::upper_diagonal{0}},
8,
Expand Down Expand Up @@ -223,7 +223,7 @@ static auto dna4_04 = []()
"AAAAAA"_dna4,
"CCCCCC"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}}
seqan3::mismatch_score{-5}}}
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-2},
seqan3::align_cfg::upper_diagonal{2}},
0,
Expand Down Expand Up @@ -267,7 +267,7 @@ static auto dna4_05 = []()
"AAAAAATCCCCCC"_dna4,
"CCCCCCTAAAAAA"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}}
seqan3::mismatch_score{-5}}}
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-100},
seqan3::align_cfg::upper_diagonal{0}},
24,
Expand Down Expand Up @@ -326,7 +326,7 @@ static auto dna4_06 = []()
"AAAAAATCCCCCC"_dna4,
"CCCCCCTAAAAAA"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}}
seqan3::mismatch_score{-5}}}
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{0},
seqan3::align_cfg::upper_diagonal{100}},
24,
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12 changes: 6 additions & 6 deletions test/unit/alignment/pairwise/fixture/local_affine_unbanded.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ static auto dna4_01 = []()
"AACCGGTTTAACCGGTT"_dna4,
"ACGTCTACGTA"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
11,
"GTTTA",
"GTCTA",
Expand Down Expand Up @@ -98,7 +98,7 @@ static auto dna4_02 = []()
"ACGTCTACGTA"_dna4,
"AACCGGTTTAACCGGTT"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
11,
"GTCTA",
"GTTTA",
Expand Down Expand Up @@ -164,7 +164,7 @@ static auto dna4_03 = []()
seqan3::align_cfg::method_local
| seqan3::align_cfg::gap{seqan3::gap_scheme{seqan3::gap_score{-1}, seqan3::gap_open_score{-1}}}
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{2},
seqan3::mismatch_score{-1}}},
seqan3::mismatch_score{-1}}},
9,
"ATAAGCGT",
"AT-AGAGT",
Expand Down Expand Up @@ -218,7 +218,7 @@ static auto dna4_04 = []()
"AAAAAA"_dna4,
"CCCCCC"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
0,
"",
"",
Expand Down Expand Up @@ -260,7 +260,7 @@ static auto dna4_05 = []()
"AAAAAATCCCCCC"_dna4,
"CCCCCCTAAAAAA"_dna4,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
24,
"AAAAAA",
"AAAAAA",
Expand Down Expand Up @@ -316,7 +316,7 @@ static auto rna5_01 = []()
"AAAAAAUUUUNNUUUUCCCCCC"_rna5,
"AAAAAACCCCCC"_rna5,
align_config | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
28,
"AAAAAAUUUUNNUUUUCCCCCC",
"AAAAAA----------CCCCCC",
Expand Down
8 changes: 4 additions & 4 deletions test/unit/alignment/pairwise/fixture/semi_global_affine_banded.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ static auto dna4_01_semi_first = []()
"ACGTAAAACGT"_dna4,
align_config_semi_seq1
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
10,
"ACGT---ATGT",
"ACGTAAAACGT",
Expand Down Expand Up @@ -96,7 +96,7 @@ static auto dna4_01_semi_first = []()
// "TTTTTACGTATGTCCCCC"_dna4,
// align_config_semi_seq1
// | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
// seqan3::mismatch_score{-5}}},
// seqan3::mismatch_score{-5}}},
// -13,
// "-----ACGTA--------AAACGT",
// "TTTTTACGTATGTCCCCC------",
Expand All @@ -113,7 +113,7 @@ static auto dna4_03_semi_second = []()
"ACGTAAAACGT"_dna4,
align_config_semi_seq2
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
-19,
"TTTTTACGTATGTCCCCC",
"GTAAAACGT---------",
Expand Down Expand Up @@ -162,7 +162,7 @@ static auto dna4_04_semi_second = []()
"TTTTTACGTATGTCCCCC"_dna4,
align_config_semi_seq2
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
-5,
"ACGTAAAACGT",
"------TACGT",
Expand Down
8 changes: 4 additions & 4 deletions test/unit/alignment/pairwise/fixture/semi_global_affine_unbanded.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ static auto dna4_01_semi_first = []()
"ACGTAAAACGT"_dna4,
align_config_semi_seq1
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
10,
"ACGT---ATGT",
"ACGTAAAACGT",
Expand Down Expand Up @@ -96,7 +96,7 @@ static auto dna4_02_semi_first = []()
"TTTTTACGTATGTCCCCC"_dna4,
align_config_semi_seq1
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
-13,
"-----ACGTA--------",
"TTTTTACGTATGTCCCCC",
Expand Down Expand Up @@ -162,7 +162,7 @@ static auto dna4_03_semi_second = []()
"ACGTAAAACGT"_dna4,
align_config_semi_seq2
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
-13,
"TTTTTACGTATGTCCCCC",
"-----ACGTA--------",
Expand Down Expand Up @@ -214,7 +214,7 @@ static auto dna4_04_semi_second = []()
"TTTTTACGTATGTCCCCC"_dna4,
align_config_semi_seq2
| seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}},
seqan3::mismatch_score{-5}}},
10,
"ACGTAAAACGT",
"ACGT---ATGT",
Expand Down
2 changes: 1 addition & 1 deletion test/unit/alignment/pairwise/semi_global_affine_banded_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ struct pairwise_semiglobal_affine_banded : public ::testing::Test
seqan3::align_cfg::gap{seqan3::gap_scheme{seqan3::gap_score{-1},
seqan3::gap_open_score{-10}}} |
seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}}};
seqan3::mismatch_score{-5}}};
}
};

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