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feat: add chopper fast-layout wrapper #234

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Merged
eseiler merged 1 commit into from
Jan 27, 2026
Merged

feat: add chopper fast-layout wrapper #234

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1 change: 1 addition & 0 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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12 changes: 12 additions & 0 deletions cmake/package-lock.cmake
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Expand Up @@ -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
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14 changes: 14 additions & 0 deletions include/layout/layout.hpp
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@@ -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);
3 changes: 3 additions & 0 deletions src/CMakeLists.txt
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Expand Up @@ -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}")
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12 changes: 12 additions & 0 deletions src/layout/CMakeLists.txt
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@@ -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")
21 changes: 21 additions & 0 deletions src/layout/layout.cpp
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@@ -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);
}
5 changes: 4 additions & 1 deletion src/needle.cpp
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Expand Up @@ -11,6 +11,7 @@
#include "estimate.hpp"
#include "ibf.hpp"
#include "insert.hpp"
#include "layout/layout.hpp"
#include "minimiser.hpp"
#include "shared.hpp"

Expand Down Expand Up @@ -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 "
Expand Down Expand Up @@ -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);
}
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1 change: 1 addition & 0 deletions test/cli/CMakeLists.txt
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Expand Up @@ -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.
24 changes: 24 additions & 0 deletions test/cli/layout_options_test.cpp
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// 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{});
}