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[TEST] Increase kmers in execute_layout_test for minHashes later. #338

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eseiler merged 4 commits into from
Sep 8, 2026
Merged

[TEST] Increase kmers in execute_layout_test for minHashes later. #338

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a5d689b
[TEST] Increase kmers in execute_layout_test for minHashes later.
smehringer Sep 8, 2026
2669999
[TEST] Increase number of kmers in test.
smehringer Sep 8, 2026
cc22621
[TEST] Update test to use more kmers.
smehringer Sep 8, 2026
310a7ca
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eseiler Sep 8, 2026
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123 changes: 65 additions & 58 deletions test/api/layout/execute_layout_test.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ TEST(execute_test, few_ubs)

auto simulated_input = [&](size_t const num, seqan::hibf::insert_iterator it)
{
size_t const desired_kmer_count = (num == 1) ? 880 : 475; // Estimate are 990.71 and 504.88
size_t const desired_kmer_count = (num == 1) ? 1760 : 940;
for (auto hash : std::views::iota(0u, desired_kmer_count))
it = hash;
};
Expand Down Expand Up @@ -105,16 +105,16 @@ TEST(execute_test, few_ubs)
"@ }\n"
"@}\n"
"@HIBF_CONFIG_END\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:42\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:9\n"
"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS\n"
"7\t0\t6\n"
"6\t6\t6\n"
"5\t12\t6\n"
"4\t18\t6\n"
"3\t24\t6\n"
"2\t30\t6\n"
"0\t36\t6\n"
"1\t42\t22\n"};
"7\t0\t9\n"
"6\t9\t5\n"
"5\t14\t5\n"
"4\t19\t5\n"
"3\t24\t5\n"
"2\t29\t5\n"
"0\t34\t5\n"
"1\t39\t25\n"};
std::string const actual_file{string_from_file(layout_file)};

EXPECT_EQ(actual_file, expected_file) << actual_file;
Expand All @@ -127,7 +127,7 @@ TEST(execute_test, set_default_tmax)

auto simulated_input = [&](size_t const num, seqan::hibf::insert_iterator it)
{
size_t const desired_kmer_count = (num == 1) ? 1000 : 500;
size_t const desired_kmer_count = (num == 1) ? 2000 : 1000;
for (auto hash : std::views::iota(0u, desired_kmer_count))
it = hash;
};
Expand Down Expand Up @@ -161,11 +161,11 @@ TEST(execute_test, many_ubs)
many_filenames.push_back({seqan3::detail::to_string("seq", i)});

// Creates sizes of the following series
// [100,101,...,120,222,223,...,241,343,344,...362,464,465,...,483,585,586,...,600]
// [801,802,...,820,922,923,...,941,1043,1044,...,1062,1164,1165,...,1183,1285,1286,...,1300]
// See also https://godbolt.org/z/9517eaaaG
auto simulated_input = [&](size_t const num, seqan::hibf::insert_iterator it)
{
size_t const desired_kmer_count = 101 * ((num + 20) / 20) + num;
size_t const desired_kmer_count = 101 * ((num + 20) / 20) + num + 700;
for (auto hash : std::views::iota(0u, desired_kmer_count))
it = hash;
};
Expand Down Expand Up @@ -327,52 +327,59 @@ TEST(execute_test, many_ubs)
"@}\n"
"@HIBF_CONFIG_END\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:63\n"
"#LOWER_LEVEL_IBF_0 fullest_technical_bin_idx:49\n"
"#LOWER_LEVEL_IBF_1 fullest_technical_bin_idx:18\n"
"#LOWER_LEVEL_IBF_2 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_0 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_1 fullest_technical_bin_idx:52\n"
"#LOWER_LEVEL_IBF_2 fullest_technical_bin_idx:52\n"
"#LOWER_LEVEL_IBF_3 fullest_technical_bin_idx:52\n"
"#LOWER_LEVEL_IBF_4 fullest_technical_bin_idx:31\n"
"#LOWER_LEVEL_IBF_5 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_6 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_7 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_8 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_9 fullest_technical_bin_idx:0\n"
"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS\n"
"16\t0;0\t1;5\n"
"15\t0;5\t1;4\n"
"14\t0;9\t1;4\n"
"13\t0;13\t1;4\n"
"12\t0;17\t1;4\n"
"11\t0;21\t1;4\n"
"10\t0;25\t1;4\n"
"9\t0;29\t1;4\n"
"8\t0;33\t1;4\n"
"7\t0;37\t1;4\n"
"6\t0;41\t1;4\n"
"5\t0;45\t1;4\n"
"4\t0;49\t1;3\n"
"3\t0;52\t1;3\n"
"2\t0;55\t1;3\n"
"1\t0;58\t1;3\n"
"0\t0;61\t1;3\n"
"26\t1;0\t1;9\n"
"25\t1;9\t1;9\n"
"24\t1;18\t1;8\n"
"23\t1;26\t1;8\n"
"22\t1;34\t1;8\n"
"21\t1;42\t1;8\n"
"20\t1;50\t1;8\n"
"19\t1;58\t1;2\n"
"18\t1;60\t1;2\n"
"17\t1;62\t1;2\n"
"34\t2;0\t1;8\n"
"33\t2;8\t1;8\n"
"32\t2;16\t1;8\n"
"31\t2;24\t1;8\n"
"30\t2;32\t1;8\n"
"29\t2;40\t1;8\n"
"28\t2;48\t1;8\n"
"27\t2;56\t1;8\n"
"35\t3\t1\n"
"36\t4\t1\n"
"37\t5\t1\n"
"38\t6\t1\n"
"39\t7\t1\n"
"40\t8\t1\n"
"41\t9\t1\n"
"1\t0;0\t1;32\n"
"0\t0;32\t1;32\n"
"6\t1;0\t1;13\n"
"5\t1;13\t1;13\n"
"4\t1;26\t1;13\n"
"3\t1;39\t1;13\n"
"2\t1;52\t1;12\n"
"11\t2;0\t1;13\n"
"10\t2;13\t1;13\n"
"9\t2;26\t1;13\n"
"8\t2;39\t1;13\n"
"7\t2;52\t1;12\n"
"16\t3;0\t1;13\n"
"15\t3;13\t1;13\n"
"14\t3;26\t1;13\n"
"13\t3;39\t1;13\n"
"12\t3;52\t1;12\n"
"21\t4;0\t1;16\n"
"20\t4;16\t1;15\n"
"19\t4;31\t1;11\n"
"18\t4;42\t1;11\n"
"17\t4;53\t1;11\n"
"25\t5;0\t1;16\n"
"24\t5;16\t1;16\n"
"23\t5;32\t1;16\n"
"22\t5;48\t1;16\n"
"29\t6;0\t1;16\n"
"28\t6;16\t1;16\n"
"27\t6;32\t1;16\n"
"26\t6;48\t1;16\n"
"33\t7;0\t1;16\n"
"32\t7;16\t1;16\n"
"31\t7;32\t1;16\n"
"30\t7;48\t1;16\n"
"37\t8;0\t1;16\n"
"36\t8;16\t1;16\n"
"35\t8;32\t1;16\n"
"34\t8;48\t1;16\n"
"41\t9;0\t1;18\n"
"40\t9;18\t1;18\n"
"39\t9;36\t1;14\n"
"38\t9;50\t1;14\n"
"42\t10\t1\n"
"43\t11\t1\n"
"44\t12\t1\n"
Expand Down
123 changes: 65 additions & 58 deletions test/api/layout/execute_with_estimation_test.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ TEST(execute_estimation_test, few_ubs)

auto simulated_input = [&](size_t const num, seqan::hibf::insert_iterator it)
{
size_t const desired_kmer_count = (num == 1) ? 1000 : 500;
size_t const desired_kmer_count = (num == 1) ? 1700 : 1200;
for (auto hash : std::views::iota(0u, desired_kmer_count))
it = hash;
};
Expand Down Expand Up @@ -78,7 +78,7 @@ TEST(execute_estimation_test, few_ubs)
## (l*m)_tmax : Computed by l_tmax * m_tmax
## size : The expected total size of an tmax-HIBF
# tmax c_tmax l_tmax m_tmax (l*m)_tmax size
64 1.00 1.00 1.00 1.00 15.7KiB
64 1.00 1.00 1.00 1.00 38.2KiB
# Best t_max (regarding expected query runtime): 64
)expected_cout");
}
Expand All @@ -95,11 +95,11 @@ TEST(execute_estimation_test, many_ubs)
many_filenames.push_back({seqan3::detail::to_string("seq", i)});

// Creates sizes of the following series
// [100,101,...,120,222,223,...,241,343,344,...362,464,465,...,483,585,586,...,600]
// [801,802,...,820,922,923,...,941,1043,1044,...,1062,1164,1165,...,1183,1285,1286,...,1300]
// See also https://godbolt.org/z/9517eaaaG
auto simulated_input = [&](size_t const num, seqan::hibf::insert_iterator it)
{
size_t const desired_kmer_count = 101 * ((num + 20) / 20) + num;
size_t const desired_kmer_count = 101 * ((num + 20) / 20) + num + 700;
for (auto hash : std::views::iota(0u, desired_kmer_count))
it = hash;
};
Expand Down Expand Up @@ -139,8 +139,8 @@ TEST(execute_estimation_test, many_ubs)
## (l*m)_tmax : Computed by l_tmax * m_tmax
## size : The expected total size of an tmax-HIBF
# tmax c_tmax l_tmax m_tmax (l*m)_tmax size
64 1.00 1.17 1.00 1.17 55.5KiB
128 1.22 1.31 1.05 1.37 58.2KiB
64 1.00 1.36 1.00 1.36 269.0KiB
128 1.22 1.42 1.00 1.42 269.8KiB
# Best t_max (regarding expected query runtime): 64
)expected_cout");

Expand Down Expand Up @@ -288,52 +288,59 @@ TEST(execute_estimation_test, many_ubs)
"@}\n"
"@HIBF_CONFIG_END\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:63\n"
"#LOWER_LEVEL_IBF_0 fullest_technical_bin_idx:49\n"
"#LOWER_LEVEL_IBF_1 fullest_technical_bin_idx:18\n"
"#LOWER_LEVEL_IBF_2 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_0 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_1 fullest_technical_bin_idx:52\n"
"#LOWER_LEVEL_IBF_2 fullest_technical_bin_idx:52\n"
"#LOWER_LEVEL_IBF_3 fullest_technical_bin_idx:52\n"
"#LOWER_LEVEL_IBF_4 fullest_technical_bin_idx:31\n"
"#LOWER_LEVEL_IBF_5 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_6 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_7 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_8 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_9 fullest_technical_bin_idx:0\n"
"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS\n"
"16\t0;0\t1;5\n"
"15\t0;5\t1;4\n"
"14\t0;9\t1;4\n"
"13\t0;13\t1;4\n"
"12\t0;17\t1;4\n"
"11\t0;21\t1;4\n"
"10\t0;25\t1;4\n"
"9\t0;29\t1;4\n"
"8\t0;33\t1;4\n"
"7\t0;37\t1;4\n"
"6\t0;41\t1;4\n"
"5\t0;45\t1;4\n"
"4\t0;49\t1;3\n"
"3\t0;52\t1;3\n"
"2\t0;55\t1;3\n"
"1\t0;58\t1;3\n"
"0\t0;61\t1;3\n"
"26\t1;0\t1;9\n"
"25\t1;9\t1;9\n"
"24\t1;18\t1;8\n"
"23\t1;26\t1;8\n"
"22\t1;34\t1;8\n"
"21\t1;42\t1;8\n"
"20\t1;50\t1;8\n"
"19\t1;58\t1;2\n"
"18\t1;60\t1;2\n"
"17\t1;62\t1;2\n"
"34\t2;0\t1;8\n"
"33\t2;8\t1;8\n"
"32\t2;16\t1;8\n"
"31\t2;24\t1;8\n"
"30\t2;32\t1;8\n"
"29\t2;40\t1;8\n"
"28\t2;48\t1;8\n"
"27\t2;56\t1;8\n"
"35\t3\t1\n"
"36\t4\t1\n"
"37\t5\t1\n"
"38\t6\t1\n"
"39\t7\t1\n"
"40\t8\t1\n"
"41\t9\t1\n"
"1\t0;0\t1;32\n"
"0\t0;32\t1;32\n"
"6\t1;0\t1;13\n"
"5\t1;13\t1;13\n"
"4\t1;26\t1;13\n"
"3\t1;39\t1;13\n"
"2\t1;52\t1;12\n"
"11\t2;0\t1;13\n"
"10\t2;13\t1;13\n"
"9\t2;26\t1;13\n"
"8\t2;39\t1;13\n"
"7\t2;52\t1;12\n"
"16\t3;0\t1;13\n"
"15\t3;13\t1;13\n"
"14\t3;26\t1;13\n"
"13\t3;39\t1;13\n"
"12\t3;52\t1;12\n"
"21\t4;0\t1;16\n"
"20\t4;16\t1;15\n"
"19\t4;31\t1;11\n"
"18\t4;42\t1;11\n"
"17\t4;53\t1;11\n"
"25\t5;0\t1;16\n"
"24\t5;16\t1;16\n"
"23\t5;32\t1;16\n"
"22\t5;48\t1;16\n"
"29\t6;0\t1;16\n"
"28\t6;16\t1;16\n"
"27\t6;32\t1;16\n"
"26\t6;48\t1;16\n"
"33\t7;0\t1;16\n"
"32\t7;16\t1;16\n"
"31\t7;32\t1;16\n"
"30\t7;48\t1;16\n"
"37\t8;0\t1;16\n"
"36\t8;16\t1;16\n"
"35\t8;32\t1;16\n"
"34\t8;48\t1;16\n"
"41\t9;0\t1;18\n"
"40\t9;18\t1;18\n"
"39\t9;36\t1;14\n"
"38\t9;50\t1;14\n"
"42\t10\t1\n"
"43\t11\t1\n"
"44\t12\t1\n"
Expand Down Expand Up @@ -404,10 +411,10 @@ TEST(execute_estimation_test, many_ubs_force_all)
for (size_t i{0}; i < 96u; ++i)
many_filenames.push_back({seqan3::detail::to_string("seq", i)});

// There are 20 files with a count of {100,200,300,400} each. There are 16 files with count 500.
// There are 20 files with counts of {800,900,1000,1100} each. There are 16 files with count 1200.
auto simulated_input = [&](size_t const num, seqan::hibf::insert_iterator it)
{
size_t const desired_kmer_count = 100 * ((num + 20) / 20);
size_t const desired_kmer_count = 100 * ((num + 20) / 20) + 700;
for (auto hash : std::views::iota(0u, desired_kmer_count))
it = hash;
};
Expand Down Expand Up @@ -447,14 +454,14 @@ TEST(execute_estimation_test, many_ubs_force_all)
## (l*m)_tmax : Computed by l_tmax * m_tmax
## size : The expected total size of an tmax-HIBF
# tmax c_tmax l_tmax m_tmax (l*m)_tmax size
64 1.00 1.18 1.00 1.18 48.0KiB
128 1.22 1.31 1.02 1.33 48.7KiB
256 1.33 1.33 1.20 1.60 57.5KiB
# Best t_max (regarding expected query runtime): 64
64 1.00 1.37 1.00 1.37 256.7KiB
128 1.22 1.43 0.99 1.42 255.3KiB
256 1.33 1.33 0.81 1.07 206.7KiB
# Best t_max (regarding expected query runtime): 256
)expected_cout");

std::string const layout_string{string_from_file(layout_file)};
EXPECT_NE(layout_string.find("\"tmax\": 64,"), std::string::npos);
EXPECT_NE(layout_string.find("\"tmax\": 256,"), std::string::npos);
}

struct dna4_traits3 : public seqan3::sequence_file_input_default_traits_dna
Expand Down
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