Sample read with two lengths, use 19-mers, reduce reference size.

.gitignore

@@ -36,7 +36,6 @@
 
 # Metadata files
 all_bin_paths.txt
-bin_paths*.txt
 example_data/*
 
 

test/cli/CMakeLists.txt

@@ -34,20 +34,20 @@ target_use_datasources (valik_test FILES 0overlap16bins.txt)
 target_use_datasources (valik_test FILES 20overlap16bins.txt)
 target_use_datasources (valik_test FILES chromosome_metadata.txt)
 
-target_use_datasources (valik_test FILES 8bins20window.ibf)
+target_use_datasources (valik_test FILES 8bins19window.ibf)
 target_use_datasources (valik_test FILES 8bins23window.ibf)
-target_use_datasources (valik_test FILES 8bins20window0error50pattern1overlap.out)
-target_use_datasources (valik_test FILES 8bins20window0error50pattern40overlap.out)
-target_use_datasources (valik_test FILES 8bins20window1error50pattern1overlap.out)
-target_use_datasources (valik_test FILES 8bins20window1error50pattern40overlap.out)
+target_use_datasources (valik_test FILES 8bins19window0error50pattern1overlap.out)
+target_use_datasources (valik_test FILES 8bins19window0error50pattern40overlap.out)
+target_use_datasources (valik_test FILES 8bins19window1error50pattern1overlap.out)
+target_use_datasources (valik_test FILES 8bins19window1error50pattern40overlap.out)
 target_use_datasources (valik_test FILES 8bins23window0error50pattern1overlap.out)
 target_use_datasources (valik_test FILES 8bins23window0error50pattern40overlap.out)
 target_use_datasources (valik_test FILES 8bins23window1error50pattern1overlap.out)
 target_use_datasources (valik_test FILES 8bins23window1error50pattern40overlap.out)
-target_use_datasources (valik_test FILES 8bins20window0error100pattern1overlap.out)
-target_use_datasources (valik_test FILES 8bins20window0error100pattern40overlap.out)
-target_use_datasources (valik_test FILES 8bins20window1error100pattern1overlap.out)
-target_use_datasources (valik_test FILES 8bins20window1error100pattern40overlap.out)
+target_use_datasources (valik_test FILES 8bins19window0error100pattern1overlap.out)
+target_use_datasources (valik_test FILES 8bins19window0error100pattern40overlap.out)
+target_use_datasources (valik_test FILES 8bins19window1error100pattern1overlap.out)
+target_use_datasources (valik_test FILES 8bins19window1error100pattern40overlap.out)
 target_use_datasources (valik_test FILES 8bins23window0error100pattern1overlap.out)
 target_use_datasources (valik_test FILES 8bins23window0error100pattern40overlap.out)
 target_use_datasources (valik_test FILES 8bins23window1error100pattern1overlap.out)

test/cli/valik_options_test.cpp

@@ -289,7 +289,7 @@ TEST_F(argparse_search, pattern_window)
 {
     cli_test_result const result = execute_app("valik", "search",
                                                          "--query ", data("query.fq"),
-                                                         "--index ", data("8bins20window.ibf"),
+                                                         "--index ", data("8bins19window.ibf"),
                                                          "--output search.out",
 							                             "--pattern 12");
     EXPECT_NE(result.exit_code, 0);

test/cli/valik_test.cpp

@@ -65,9 +65,9 @@ TEST_P(valik_build, build_with_file)
     }
 
     cli_test_result const result = execute_app("valik", "build",
-                                                         "--kmer 20",
+                                                         "--kmer 19",
                                                          "--window ", std::to_string(window_size),
-                                                         "--size 100k",
+                                                         "--size 32k",
                                                          "--threads ", run_parallel ? "2" : "1",
                                                          "--output index.ibf",
                                                          "bin_paths.txt");
@@ -81,7 +81,7 @@ TEST_P(valik_build, build_with_file)
 
 INSTANTIATE_TEST_SUITE_P(build_suite,
                          valik_build,
-                         testing::Combine(testing::Values(8), testing::Values(20, 23), testing::Values(true, false)),
+                         testing::Combine(testing::Values(8), testing::Values(19, 23), testing::Values(true, false)),
                          [] (testing::TestParamInfo<valik_build::ParamType> const & info)
                          {
                              std::string name = std::to_string(std::get<0>(info.param)) + "_bins_" +
@@ -121,14 +121,14 @@ TEST_P(valik_search, search)
 
 INSTANTIATE_TEST_SUITE_P(search_suite,
                          valik_search,
-                         testing::Combine(testing::Values(8), testing::Values(20, 23), testing::Values(0, 1),
+                         testing::Combine(testing::Values(8), testing::Values(19, 23), testing::Values(0, 1),
 				 testing::Values(50, 100), testing::Values(1, 40)),
                          [] (testing::TestParamInfo<valik_search::ParamType> const & info)
                          {
                              std::string name = std::to_string(std::get<0>(info.param)) + "_bins_" +
                                                 std::to_string(std::get<1>(info.param)) + "_window_" +
                                                 std::to_string(std::get<2>(info.param)) + "_error_" +
-						std::to_string(std::get<3>(info.param)) + "_pattern_" +
-						std::to_string(std::get<4>(info.param)) + "_overlap";
+						                        std::to_string(std::get<3>(info.param)) + "_pattern_" +
+						                        std::to_string(std::get<4>(info.param)) + "_overlap";
                              return name;
                          });

test/data/.gitignore

@@ -1,2 +1,2 @@
 *example*
-CMakeFiles/*
+CMakeFiles/*