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[TEST] Increase seq1/2/3.fa and small.fa sequences and remove unused files in data/ #340

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[TEST] Increase seq1/2/3.fa and small.fa sequences and remove unused files in data/ #340

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ea79ce3
[TEST] Increased sizes of examples files and adapted tests.
smehringer Sep 10, 2026
aeab599
[TEST] Remove unused data files.
smehringer Sep 10, 2026
52d5371
[TEST] Redefine small.minimiser to dummy.minimiser.
smehringer Sep 10, 2026
8b876a3
[TEST] Remove legacy data/small_graph.dot
smehringer Sep 10, 2026
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12 changes: 6 additions & 6 deletions test/api/layout/execute_with_estimation_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -553,16 +553,16 @@ TEST(execute_estimation_test, with_rearrangement)

#ifdef _LIBCPP_VERSION // seqan::hibf::sketch::toolbox::sort_by_cardinalities is not stable
result +=
R"expected_cout(64 1.00 2.26 1.00 2.26 110.5KiB
128 1.22 1.96 1.08 2.11 118.9KiB
256 1.33 1.66 1.18 1.97 130.9KiB
R"expected_cout(64 1.00 1.66 1.00 1.66 4.5MiB
128 1.22 1.78 1.15 2.05 5.2MiB
256 1.33 1.48 1.36 2.01 6.2MiB
# Best t_max (regarding expected query runtime): 256
)expected_cout";
#else
result +=
R"expected_cout(64 1.00 2.34 1.00 2.34 110.1KiB
128 1.22 2.01 1.08 2.17 118.9KiB
256 1.33 1.76 1.39 2.44 152.7KiB
R"expected_cout(64 1.00 1.65 1.00 1.65 4.5MiB
128 1.22 1.78 1.15 2.05 5.2MiB
256 1.33 1.48 1.36 2.01 6.2MiB
# Best t_max (regarding expected query runtime): 256
)expected_cout";
#endif
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2 changes: 1 addition & 1 deletion test/api/sketch/CMakeLists.txt
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Expand Up @@ -11,7 +11,7 @@ add_api_test (check_filenames_test.cpp)
target_use_datasources (check_filenames_test FILES seq1.fa)
target_use_datasources (check_filenames_test FILES seq2.fa)
target_use_datasources (check_filenames_test FILES seq3.fa)
target_use_datasources (check_filenames_test FILES small.minimiser)
target_use_datasources (check_filenames_test FILES dummy.minimiser)

add_api_test (read_data_file_test.cpp)
target_use_datasources (read_data_file_test FILES seqinfo.tsv)
10 changes: 5 additions & 5 deletions test/api/sketch/check_filenames_test.cpp
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Expand Up @@ -42,9 +42,9 @@ TEST(check_filenames_test, overload)

TEST(check_filenames_test, minimiser_filenames)
{
std::vector<std::string> filenames{data("small.minimiser").string(),
data("small.minimiser").string(),
data("small.minimiser").string()};
std::vector<std::string> filenames{data("dummy.minimiser").string(),
data("dummy.minimiser").string(),
data("dummy.minimiser").string()};

chopper::configuration config;

Expand All @@ -55,7 +55,7 @@ TEST(check_filenames_test, minimiser_filenames)

TEST(check_filenames_test, mixed_filenames_sequence_files)
{
std::vector<std::string> filenames{data("seq2.fa").string(), data("small.minimiser").string()};
std::vector<std::string> filenames{data("seq2.fa").string(), data("dummy.minimiser").string()};

chopper::configuration config;

Expand All @@ -64,7 +64,7 @@ TEST(check_filenames_test, mixed_filenames_sequence_files)

TEST(check_filenames_test, mixed_filenames_minimiser_files)
{
std::vector<std::string> filenames{data("small.minimiser").string(), data("seq2.fa").string()};
std::vector<std::string> filenames{data("dummy.minimiser").string(), data("seq2.fa").string()};

chopper::configuration config;

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2 changes: 0 additions & 2 deletions test/cli/CMakeLists.txt
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Expand Up @@ -12,8 +12,6 @@ add_cli_test (cli_chopper_basic_test.cpp)
add_cli_test (cli_chopper_pipeline_test.cpp)
target_use_datasources (cli_chopper_pipeline_test FILES seq1.fa)
target_use_datasources (cli_chopper_pipeline_test FILES small.fa)
target_use_datasources (cli_chopper_pipeline_test FILES small2.fa)
target_use_datasources (cli_chopper_pipeline_test FILES small.split)

add_cli_test (cli_chopper_layout_from_sketch_file.cpp)
target_use_datasources (cli_chopper_layout_from_sketch_file FILES seq1.fa)
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10 changes: 5 additions & 5 deletions test/cli/cli_chopper_layout_from_sketch_file.cpp
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Expand Up @@ -123,12 +123,12 @@ TEST_F(cli_test, chopper_layout_from_sketch_file)
"@ }\n"
"@}\n"
"@HIBF_CONFIG_END\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:16\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:0\n"
"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS\n"
"1\t0\t16\n"
"3\t16\t23\n"
"2\t39\t15\n"
"0\t54\t10\n"};
"1\t0\t9\n"
"0\t9\t8\n"
"2\t17\t8\n"
"3\t25\t39\n"};

std::string const actual_file{string_from_file(binning_filename)};
EXPECT_EQ(actual_file, expected_file);
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10 changes: 5 additions & 5 deletions test/cli/cli_chopper_pipeline_test.cpp
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Expand Up @@ -208,12 +208,12 @@ TEST_F(cli_test, chopper_layout2)
"@ }\n"
"@}\n"
"@HIBF_CONFIG_END\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:16\n"
"#TOP_LEVEL_IBF fullest_technical_bin_idx:0\n"
"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS\n"
"1\t0\t16\n"
"3\t16\t23\n"
"2\t39\t15\n"
"0\t54\t10\n"};
"1\t0\t9\n"
"0\t9\t8\n"
"2\t17\t8\n"
"3\t25\t39\n"};

std::string const actual_file{string_from_file(binning_filename)};
EXPECT_EQ(actual_file, expected_file);
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20 changes: 10 additions & 10 deletions test/cli/util_display_layout_test.cpp
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Expand Up @@ -123,10 +123,10 @@ TEST_F(cli_test, display_layout_general)
std::string expected_general_file{
"# Layout: " + layout_filename.string() + "\n" +
R"(tb_index exact_size estimated_size fpr_corrected_size shared_size ub_count kind splits
0 479 483 153 0 2 merged 1
1 466 466 466 0 1 split 1
2 287 289 420 0 1 split 2
3 287 289 420 0 1 split 0
0 32291 32795 10301 0 2 merged 1
1 15984 15884 15984 0 1 split 1
2 17745 17971 25914 0 1 split 2
3 17745 17971 25914 0 1 split 0
)"};

std::string const actual_file{string_from_file(general_filename)};
Expand Down Expand Up @@ -168,10 +168,10 @@ TEST_F(cli_test, display_layout_general_with_shared_kmers)
std::string expected_general_file{
"# Layout: " + layout_filename.string() + "\n" +
R"(tb_index exact_size estimated_size fpr_corrected_size shared_size ub_count kind splits
0 479 483 153 371 2 merged 1
1 466 466 466 0 1 split 1
2 287 289 420 0 1 split 2
3 287 289 420 0 1 split 0
0 32291 32795 10301 0 2 merged 1
1 15984 15884 15984 0 1 split 1
2 17745 17971 25914 0 1 split 2
3 17745 17971 25914 0 1 split 0
)"};

std::string const actual_file{string_from_file(general_filename)};
Expand Down Expand Up @@ -211,8 +211,8 @@ TEST_F(cli_test, display_layout_sizes)
std::string expected_general_file{R"(# Levels: 2
# User bins: 4
LEVEL BIT_SIZE IBFS AVG_LOAD_FACTOR TBS_TOO_BIG AVG_TBS_TOO_BIG_ELEMENTS AVG_MAX_ELEMENTS
0 4832 1 79.44 0 0 479
1 8916 1 80.26 0 0 385
0 325572 1 64.85 0 0 32291
1 354192 1 77.61 0 0 15345
)"};

std::string const actual_file{string_from_file(sizes_filename)};
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32 changes: 6 additions & 26 deletions test/data/datasources.cmake
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Expand Up @@ -9,46 +9,26 @@ cmake_minimum_required (VERSION 3.18)

include (cmake/app_datasources.cmake)

declare_datasource (FILE small_graph.dot URL ${CMAKE_SOURCE_DIR}/test/data/small_graph.dot URL_HASH
SHA256=f573bb45abe677bda78d5f700bd6a9b5f2415f405953f5c085be491e2598f02e
)

declare_datasource (FILE small.fa URL ${CMAKE_SOURCE_DIR}/test/data/small.fa URL_HASH
SHA256=215a646ccd2d156eeabdd792108fc0ba385e244a25218afc095658189d2a3c0d
SHA256=41d7eace7e07335afe6aa2c3b313eacae828e0f42a876fe97bf74a4cef4323f9
)

declare_datasource (FILE seq1.fa URL ${CMAKE_SOURCE_DIR}/test/data/seq1.fa URL_HASH
SHA256=f60b985d9f3be1d3dd6105d62f4321eeb617bc52f4fb0435b016bf1873aa2eac
SHA256=752f6ff662e9c325886aab84db998c63fc89d7ff2f4504ccd686fd853e67a003
)

declare_datasource (FILE seq2.fa URL ${CMAKE_SOURCE_DIR}/test/data/seq2.fa URL_HASH
SHA256=4153dfac5993b6ddeebf76fabeaaaad838b68f4abe0c3c03cc95b9196832af7a
SHA256=c9c402bcb982a7f3ecb0ef8810b8d4ae3050553faa295a6c3e538713199564dd
)

declare_datasource (FILE seq3.fa URL ${CMAKE_SOURCE_DIR}/test/data/seq3.fa URL_HASH
SHA256=aa440a61539216096680e53a1d68b245e5a7cac67e7eca315996d51b863d9915
)

declare_datasource (FILE small2.fa URL ${CMAKE_SOURCE_DIR}/test/data/small2.fa URL_HASH
SHA256=3a444c41f71586d62514eea8faf3c699ac5f2cfce94fd3fc7c3e47d3ff3a8383
SHA256=24a275e4666f815e46d1ccfb135bce5ea794f6630c8ffd9117eb0dcecce9d414
)

declare_datasource (FILE seqinfo.tsv URL ${CMAKE_SOURCE_DIR}/test/data/seqinfo.tsv URL_HASH
SHA256=c6e28cc4ebf4902c41b1c237b1410665994e0fd0b8d8473c38a8107041d78172
)

declare_datasource (FILE small.split URL ${CMAKE_SOURCE_DIR}/test/data/small.split URL_HASH
SHA256=b7f8ae432149580c4be0f349f2e2ee2f33bee44b3cadb436f344a643e5a41945
)

declare_datasource (FILE small.hll URL ${CMAKE_SOURCE_DIR}/test/data/small.hll URL_HASH
SHA256=039d7bdbb70e4d98285c09bbbcb2cd1fafb8038689c270cf231debb248c59206
)

declare_datasource (FILE small2.hll URL ${CMAKE_SOURCE_DIR}/test/data/small2.hll URL_HASH
SHA256=039d7bdbb70e4d98285c09bbbcb2cd1fafb8038689c270cf231debb248c59206
)

declare_datasource (FILE small.minimiser URL ${CMAKE_SOURCE_DIR}/test/data/small.minimiser URL_HASH
SHA256=6262de00ad97113320469ff952e657930d07151bda5174ee3599560eccb6f0e1
declare_datasource (FILE dummy.minimiser URL ${CMAKE_SOURCE_DIR}/test/data/dummy.minimiser URL_HASH
SHA256=7514acab108f7e5dc7cf048690dc153c13b8a2f2df7cab6d755638cd16ea79b1
)
1 change: 1 addition & 0 deletions test/data/dummy.minimiser
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@@ -0,0 +1 @@
dummy file. This is not a real minimiser file because the current test only checks the filename extension
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