[INFRA] Update raptor to the latest main in the HIBF lib and chopper. (…

…#429)

* [INFRA] Update raptor to the latest main in the HIBF lib and chopper.

* more

* fix

cmake/package-lock.cmake

@@ -6,7 +6,7 @@
 # This file should be committed to version control
 
 # hibf
-set (RAPTOR_HIBF_VERSION 2ee8fa371f20cfc170ccf01bc3d50fce1ecd22fa)
+set (RAPTOR_HIBF_VERSION ed7fc7126375f350d886bb09daa14f26b2b9d356)
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${RAPTOR_HIBF_VERSION}
@@ -36,7 +36,7 @@ CPMDeclarePackage (seqan3
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # chopper
-set (RAPTOR_CHOPPER_VERSION 40b79a02a44d66bc0bd98d50e731a93ab38e96f5)
+set (RAPTOR_CHOPPER_VERSION f48073b8b440b30f46075a31aaeee3818e180cd6)
 CPMDeclarePackage (chopper
                    NAME chopper
                    GIT_TAG ${RAPTOR_CHOPPER_VERSION}

src/layout/raptor_layout.cpp

@@ -7,11 +7,8 @@
  * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
  */
 
-#include <chopper/input_functor.hpp>
-#include <chopper/layout/execute.hpp>
+#include <chopper/chopper_layout.hpp>
 #include <chopper/set_up_parser.hpp>
-#include <chopper/sketch/check_filenames.hpp>
-#include <chopper/sketch/read_data_file.hpp>
 
 #include <raptor/argument_parsing/init_shared_meta.hpp>
 
@@ -27,30 +24,7 @@ void chopper_layout(sharg::parser & parser)
     parser.info.author = "Svenja Mehringer";
     parser.info.email = "[email protected]";
 
-    parser.parse();
-
-    if (!parser.is_option_set("window"))
-        config.window_size = config.k;
-    else if (config.k > config.window_size)
-        throw sharg::parser_error{"The k-mer size cannot be bigger than the window size."};
-
-    config.disable_sketch_output = !parser.is_option_set("output-sketches-to");
-
-    if (std::filesystem::is_empty(config.data_file))
-        throw sharg::parser_error{"The input file is empty."};
-
-    std::vector<std::vector<std::string>> filenames{};
-    chopper::sketch::read_data_file(config, filenames);
-
-    chopper::sketch::check_filenames(filenames, config);
-
-    config.hibf_config.input_fn = chopper::input_functor{.filenames = filenames,
-                                                         .input_are_precomputed_files = config.precomputed_files,
-                                                         .kmer_size = config.k,
-                                                         .window_size = config.window_size};
-    config.hibf_config.number_of_user_bins = filenames.size();
-
-    chopper::layout::execute(config, filenames);
+    chopper::chopper_layout(config, parser);
 }
 
 } // namespace raptor

test/unit/cli/argument_parsing/options_test.cpp

@@ -118,7 +118,7 @@ TEST_F(argparse_layout, no_bins_in_file)
 {
     cli_test_result const result = execute_app("raptor", "layout", "--input", tmp_bin_list_empty);
     EXPECT_EQ(result.out, std::string{});
-    EXPECT_EQ(result.err, std::string{"[Error] The input file is empty.\n"});
+    EXPECT_EQ(result.err, "[Error] The file " + tmp_bin_list_empty.string() + " appears to be empty.\n");
     RAPTOR_ASSERT_FAIL_EXIT(result);
 }