[MISC] Default should be w=k if no w given

include/chopper/configuration.hpp

@@ -41,7 +41,7 @@ struct configuration
     uint8_t k{19};
 
     //!\brief The window size to compute minimizers before computing a HyperLogLog sketch from them.
-    uint8_t window_size{19};
+    uint8_t window_size{k};
 
     //!\brief Do not write the sketches into a dedicated directory.
     bool disable_sketch_output{false};

src/chopper.cpp

@@ -34,6 +34,11 @@ int main(int argc, char const * argv[])
     {
         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");
     }
     catch (sharg::parser_error const & ext) // the user did something wrong

src/set_up_parser.cpp

@@ -75,7 +75,9 @@ void set_up_parser(sharg::parser & parser, configuration & config)
                 "runtime performance. On the other hand, it also decreases accuracy and might cause false negatives."
                 "For DNA sequences, a window size of 2-4 positions more than the kmers size, e.g. (42,20)-minimizers, "
                 "has proven to reduce the computational effort significantly while only slightly descreasing the "
-                "accuracy."});
+                "accuracy.",
+            .default_message = "k-mer size",
+        });
 
     parser.add_option(
         config.hibf_config.tmax,

test/cli/cli_chopper_pipeline_test.cpp

@@ -75,6 +75,7 @@ TEST_F(cli_test, chopper_layout)
                                       "@            \"value0\": \"\"\n"
                                       "@        },\n"
                                       "@        \"k\": 15,\n"
+                                      "@        \"window_size\": 15,\n"
                                       "@        \"disable_sketch_output\": true,\n"
                                       "@        \"precomputed_files\": false,\n"
                                       "@        \"output_filename\": {\n"