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[TEST] add input_test.cpp with read_layouts_file. #235

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merged 4 commits into from
Nov 28, 2023
Merged

[TEST] add input_test.cpp with read_layouts_file. #235

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fb5881f
[TEST] add input_test.cpp with read_layouts_file.
smehringer Nov 14, 2023
ea02851
fix name
smehringer Nov 28, 2023
18596db
fix
smehringer Nov 28, 2023
04e8e79
remove workaround
eseiler Nov 28, 2023
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1 change: 1 addition & 0 deletions test/api/layout/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,4 @@ target_use_datasources (execute_with_estimation_test FILES small.fa)

add_api_test (hibf_statistics_test.cpp)
add_api_test (user_bin_io_test.cpp)
add_api_test (input_test.cpp)
83 changes: 83 additions & 0 deletions test/api/layout/input_test.cpp
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@@ -0,0 +1,83 @@
#include <gtest/gtest.h> // for Test, TestInfo, EXPECT_EQ, Message, TEST, TestPartResult

#include <sstream> // for operator<<, char_traits, basic_ostream, basic_stringstream, strings...
#include <string> // for allocator, string
#include <vector> // for vector

#include <chopper/layout/input.hpp>

std::string const layout_header{"@CHOPPER_USER_BINS\n"
"@0 seq0.fa\n"
"@1 seq1.fa\n"
"@2 seq2.fa\n"
"@3 seq3.fa\n"
"@4 seq4.fa\n"
"@5 seq5.fa\n"
"@6 seq6.fa\n"
"@7 seq7.fa\n"
"@CHOPPER_USER_BINS_END\n"
"@CHOPPER_CONFIG\n"
"@{\n"
"@ \"chopper_config\": {\n"
"@ \"version\": 2,\n"
"@ \"data_file\": {\n"
"@ \"value0\": \"input.txt\"\n"
"@ },\n"
"@ \"debug\": false,\n"
"@ \"sketch_directory\": {\n"
"@ \"value0\": \"\"\n"
"@ },\n"
"@ \"k\": 15,\n"
"@ \"window_size\": 15,\n"
"@ \"disable_sketch_output\": true,\n"
"@ \"precomputed_files\": false,\n"
"@ \"output_filename\": {\n"
"@ \"value0\": \"foo.layout\"\n"
"@ },\n"
"@ \"determine_best_tmax\": false,\n"
"@ \"force_all_binnings\": false\n"
"@ }\n"
"@}\n"
"@CHOPPER_CONFIG_END\n"
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 1,\n"
"@ \"number_of_user_bins\": 3,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
"@ \"relaxed_fpr\": 0.3,\n"
"@ \"threads\": 2,\n"
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": false,\n"
"@ \"disable_rearrangement\": false\n"
"@ }\n"
"@}\n"
"@HIBF_CONFIG_END\n"};

TEST(layout_test, read_single_layout)
{
// layout consists of three partitions, written one after the other
std::stringstream ss{layout_header + R"layout_file(#TOP_LEVEL_IBF fullest_technical_bin_idx:111
#LOWER_LEVEL_IBF_0 fullest_technical_bin_idx:0
#LOWER_LEVEL_IBF_2 fullest_technical_bin_idx:2
#LOWER_LEVEL_IBF_1;2;3;4 fullest_technical_bin_idx:22
#USER_BIN_IDX TECHNICAL_BIN_INDICES NUMBER_OF_TECHNICAL_BINS
7 0 1
4 1;0 1;22
5 1;2;3;4;22 1;1;1;1;21
)layout_file"};

auto [filenames, chopper_config, layout] = chopper::layout::read_layout_file(ss);

EXPECT_EQ(layout.top_level_max_bin_id, 111);
EXPECT_EQ(layout.max_bins[0], (seqan::hibf::layout::layout::max_bin{{0}, 0}));
EXPECT_EQ(layout.max_bins[1], (seqan::hibf::layout::layout::max_bin{{2}, 2}));
EXPECT_EQ(layout.max_bins[2], (seqan::hibf::layout::layout::max_bin{{1, 2, 3, 4}, 22}));
EXPECT_EQ(layout.user_bins[0], (seqan::hibf::layout::layout::user_bin{std::vector<size_t>{}, 0, 1, 7}));
EXPECT_EQ(layout.user_bins[1], (seqan::hibf::layout::layout::user_bin{std::vector<size_t>{1}, 0, 22, 4}));
EXPECT_EQ(layout.user_bins[2], (seqan::hibf::layout::layout::user_bin{std::vector<size_t>{1, 2, 3, 4}, 22, 21, 5}));
}