feat: add chopper fast-layout wrapper

Author: eseiler

CMakeLists.txt

@@ -74,6 +74,7 @@ CPMGetPackage (use_ccache)
 CPMGetPackage (seqan3)
 CPMGetPackage (sharg)
 CPMGetPackage (hibf)
+CPMGetPackage (chopper)
 
 # Add the application. This will include `src/CMakeLists.txt`.
 add_subdirectory (src)

cmake/package-lock.cmake

@@ -18,6 +18,18 @@ CPMDeclarePackage (hibf
                    OPTIONS "INSTALL_HIBF OFF"
 )
 
+# chopper
+set (NEEDLE_CHOPPER_VERSION 0d03e6e80bd4f4ce82eaa8b059590de2bf7d4f7c CACHE STRING "")
+CPMDeclarePackage (chopper
+                   NAME chopper
+                   GIT_TAG ${NEEDLE_CHOPPER_VERSION} # fast_layout_newest_only_fast_layout
+                   GITHUB_REPOSITORY smehringer/chopper
+                   SYSTEM TRUE
+                   OPTIONS "CHOPPER_INSTALL OFF" "CHOPPER_BUILD_DOC OFF" "CHOPPER_BUILD_TEST OFF"
+                           "CMAKE_MESSAGE_LOG_LEVEL WARNING"
+                   EXCLUDE_FROM_ALL TRUE
+)
+
 # seqan3
 set (NEEDLE_SEQAN3_VERSION 3.4.0 CACHE STRING "")
 CPMDeclarePackage (seqan3

include/layout/layout.hpp

@@ -0,0 +1,14 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+/*!\file
+ * \brief Provides chopper_layout.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <sharg/parser.hpp>
+
+void chopper_layout(sharg::parser & parser);

src/CMakeLists.txt

@@ -28,8 +28,11 @@ target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC sharg::sharg)
 target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan::hibf)
 target_include_directories ("${PROJECT_NAME}_lib" PUBLIC ../include)
 
+add_subdirectory (layout)
+
 add_executable ("${PROJECT_NAME}" needle.cpp)
 target_link_libraries ("${PROJECT_NAME}" PRIVATE "${PROJECT_NAME}_lib")
+target_link_libraries ("${PROJECT_NAME}" PRIVATE "${PROJECT_NAME}_layout")
 set_target_properties ("${PROJECT_NAME}" PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 target_compile_definitions ("${PROJECT_NAME}" PRIVATE NEEDLE_VERSION="${NEEDLE_ARGPARSE_VERSION}")
 target_compile_definitions ("${PROJECT_NAME}" PRIVATE NEEDLE_DATE="${NEEDLE_ARGPARSE_DATE}")

src/layout/CMakeLists.txt

@@ -0,0 +1,12 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: BSD-3-Clause
+
+cmake_minimum_required (VERSION 3.25...3.30)
+
+if (TARGET "${PROJECT_NAME}_layout")
+    return ()
+endif ()
+
+add_library ("${PROJECT_NAME}_layout" STATIC layout.cpp)
+target_link_libraries ("${PROJECT_NAME}_layout" PRIVATE "chopper::chopper")

src/layout/layout.cpp

@@ -0,0 +1,21 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+/*!\file
+ * \brief Implements chopper_layout.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#include <chopper/chopper_layout.hpp>
+#include <chopper/set_up_parser.hpp>
+
+void chopper_layout(sharg::parser & parser)
+{
+    chopper::configuration config;
+    set_up_parser(parser, config);
+    parser.info.author = "Svenja Mehringer";
+    parser.info.email = "svenja.mehringer@fu-berlin.de";
+
+    chopper::chopper_layout(config, parser);
+}

src/needle.cpp

@@ -11,6 +11,7 @@
 #include "estimate.hpp"
 #include "ibf.hpp"
 #include "insert.hpp"
+#include "layout/layout.hpp"
 #include "minimiser.hpp"
 #include "shared.hpp"
 
@@ -618,7 +619,7 @@ int main(int argc, char const ** argv)
             argc,
             argv,
             sharg::update_notifications::on,
-            {"count", "delete", "estimate", "genome", "ibf", "ibfmin", "insert", "insertmin", "minimiser"}};
+            {"count", "delete", "estimate", "genome", "ibf", "ibfmin", "insert", "insertmin", "layout", "minimiser"}};
         add_parser_meta(needle_parser);
         needle_parser.info.description.push_back(
             "Needle allows you to build an Interleaved Bloom Filter (IBF) with the "
@@ -648,6 +649,8 @@ int main(int argc, char const ** argv)
         else if (sub_parser.info.app_name == std::string_view{"needle-insertmin"})
             throw sharg::parser_error{"This operation is not yet supported for Needle with HIBF."};
         // run_needle_insert_min(sub_parser);
+        else if (sub_parser.info.app_name == std::string_view{"needle-layout"})
+            chopper_layout(sub_parser);
         else if (sub_parser.info.app_name == std::string_view{"needle-minimiser"})
             run_needle_minimiser(sub_parser);
     }

test/cli/CMakeLists.txt

@@ -10,4 +10,5 @@ add_app_test (ibf_options_test.cpp)
 add_app_test (minimiser_options_test.cpp)
 add_app_test (estimate_options_test.cpp)
 add_app_test (count_options_test.cpp)
+add_app_test (layout_options_test.cpp)
 # add_app_test (delete_options_test.cpp) # Not yet supported for Needle with HIBF.

test/cli/layout_options_test.cpp

@@ -0,0 +1,24 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#include <string> // strings
+
+#include "../app_test.hpp"
+
+struct needle_layout_test : public app_test
+{};
+
+TEST_F(needle_layout_test, no_options)
+{
+    app_test_result result = execute_app("layout");
+    std::string expected{"needle-layout - Compute an HIBF layout\n"
+                         "======================================\n"
+                         "     --input <file> [--output <file>] [--threads <number>] [--kmer <number>]\n"
+                         "    [--fpr <number>] [--hash <number>] [--disable-estimate-union]\n"
+                         "    [--disable-rearrangement]\n"
+                         "    Try -h or --help for more information.\n"};
+    EXPECT_SUCCESS(result);
+    EXPECT_EQ(result.out, expected);
+    EXPECT_EQ(result.err, std::string{});
+}