diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index bcb8fb6d..bea13a2c 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -8,7 +8,7 @@ # cmake-format: off # hibf -set (CHOPPER_HIBF_VERSION fc4e40d8672f496a32df73c608915d45e715f6a8 CACHE STRING "") +set (CHOPPER_HIBF_VERSION bbca76409f5445f1404c206021fcfa37f1fd7054 CACHE STRING "") CPMDeclarePackage (hibf NAME hibf GIT_TAG ${CHOPPER_HIBF_VERSION} # main @@ -18,7 +18,7 @@ CPMDeclarePackage (hibf OPTIONS "INSTALL_HIBF OFF" ) # sharg -set (CHOPPER_SHARG_VERSION 1.2.1 CACHE STRING "") +set (CHOPPER_SHARG_VERSION 1.2.2 CACHE STRING "") CPMDeclarePackage (sharg NAME sharg VERSION ${CHOPPER_SHARG_VERSION} @@ -29,7 +29,7 @@ CPMDeclarePackage (sharg OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "BUILD_TESTING OFF" ) # seqan3 -set (CHOPPER_SEQAN3_VERSION 3.4.0 CACHE STRING "") +set (CHOPPER_SEQAN3_VERSION 3.4.1 CACHE STRING "") CPMDeclarePackage (seqan3 NAME seqan3 VERSION ${CHOPPER_SEQAN3_VERSION} diff --git a/test/api/config_test.cpp b/test/api/config_test.cpp index 8830da25..99bfc131 100644 --- a/test/api/config_test.cpp +++ b/test/api/config_test.cpp @@ -95,7 +95,7 @@ static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n" "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 123456789,\n" "@ \"number_of_hash_functions\": 4,\n" "@ \"maximum_fpr\": 0.0001,\n" @@ -104,6 +104,7 @@ static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n" "@ \"sketch_bits\": 8,\n" "@ \"tmax\": 128,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.0,\n" "@ \"max_rearrangement_ratio\": 0.333,\n" "@ \"disable_estimate_union\": true,\n" diff --git a/test/api/layout/execute_layout_test.cpp b/test/api/layout/execute_layout_test.cpp index 5449ec12..86d5036c 100644 --- a/test/api/layout/execute_layout_test.cpp +++ b/test/api/layout/execute_layout_test.cpp @@ -88,7 +88,7 @@ TEST(execute_test, few_ubs) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 8,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -97,6 +97,7 @@ TEST(execute_test, few_ubs) "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": true,\n" @@ -308,7 +309,7 @@ TEST(execute_test, many_ubs) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 96,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -317,6 +318,7 @@ TEST(execute_test, many_ubs) "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": true,\n" diff --git a/test/api/layout/execute_with_estimation_test.cpp b/test/api/layout/execute_with_estimation_test.cpp index c33d0243..1f7da35c 100644 --- a/test/api/layout/execute_with_estimation_test.cpp +++ b/test/api/layout/execute_with_estimation_test.cpp @@ -270,7 +270,7 @@ TEST(execute_estimation_test, many_ubs) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 96,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -279,6 +279,7 @@ TEST(execute_estimation_test, many_ubs) "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": true,\n" diff --git a/test/api/layout/input_test.cpp b/test/api/layout/input_test.cpp index f35a147c..d575ebf3 100644 --- a/test/api/layout/input_test.cpp +++ b/test/api/layout/input_test.cpp @@ -42,7 +42,7 @@ std::string const layout_header{"@CHOPPER_USER_BINS\n" "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 3,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -51,6 +51,7 @@ std::string const layout_header{"@CHOPPER_USER_BINS\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" diff --git a/test/cli/cli_chopper_layout_from_sketch_file.cpp b/test/cli/cli_chopper_layout_from_sketch_file.cpp index 16c5f5c0..65733593 100644 --- a/test/cli/cli_chopper_layout_from_sketch_file.cpp +++ b/test/cli/cli_chopper_layout_from_sketch_file.cpp @@ -108,7 +108,7 @@ TEST_F(cli_test, chopper_layout_from_sketch_file) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 4,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -117,6 +117,7 @@ TEST_F(cli_test, chopper_layout_from_sketch_file) "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" diff --git a/test/cli/cli_chopper_pipeline_test.cpp b/test/cli/cli_chopper_pipeline_test.cpp index 98520094..e8322cc2 100644 --- a/test/cli/cli_chopper_pipeline_test.cpp +++ b/test/cli/cli_chopper_pipeline_test.cpp @@ -91,7 +91,7 @@ TEST_F(cli_test, chopper_layout) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 3,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -100,6 +100,7 @@ TEST_F(cli_test, chopper_layout) "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" @@ -194,7 +195,7 @@ TEST_F(cli_test, chopper_layout2) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 4,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -203,6 +204,7 @@ TEST_F(cli_test, chopper_layout2) "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" diff --git a/test/cli/util_display_layout_test.cpp b/test/cli/util_display_layout_test.cpp index 945c0c2a..8e671d23 100644 --- a/test/cli/util_display_layout_test.cpp +++ b/test/cli/util_display_layout_test.cpp @@ -62,7 +62,7 @@ std::string get_layout_with_correct_filenames(std::string_view const seq1_filena "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 2,\n" + "@ \"version\": 3,\n" "@ \"number_of_user_bins\": 4,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -71,6 +71,7 @@ std::string get_layout_with_correct_filenames(std::string_view const seq1_filena "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 4,\n" "@ \"empty_bin_fraction\": 0.0,\n" + "@ \"track_occupancy\": false,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n"