Merge pull request #411 from eseiler/fix/layout

[FIX] Layout window size

src/layout/raptor_layout.cpp

@@ -31,6 +31,12 @@ void chopper_layout(sharg::parser & parser)
     parser.info.email = "svenja.mehringer@fu-berlin.de";
 
     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))
@@ -41,7 +47,10 @@ void chopper_layout(sharg::parser & parser)
 
     chopper::sketch::check_filenames(filenames, config);
 
-    config.hibf_config.input_fn = chopper::input_functor{filenames, config.precomputed_files, config.k};
+    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);

test/unit/cli/argument_parsing/options_test.cpp

@@ -126,6 +126,15 @@ TEST_F(argparse_layout, no_bins_in_file)
     RAPTOR_ASSERT_FAIL_EXIT(result);
 }
 
+TEST_F(argparse_layout, kmer_window)
+{
+    cli_test_result const result =
+        execute_app("raptor", "layout", "--input", tmp_bin_list_file, "--kmer 20", "--window 19");
+    EXPECT_EQ(result.out, std::string{});
+    EXPECT_EQ(result.err, std::string{"[Error] The k-mer size cannot be bigger than the window size.\n"});
+    RAPTOR_ASSERT_FAIL_EXIT(result);
+}
+
 TEST_F(argparse_build, input_missing)
 {
     cli_test_result const result = execute_app("raptor", "build", "--output ./index.raptor");