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cmake_minimum_required(VERSION 3.12)
project(spoa VERSION 4.1.5
LANGUAGES CXX
DESCRIPTION "Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment.")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
# set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build all libraries as shared")
include(FetchContent)
include(GNUInstallDirs)
include(CMakePackageConfigHelpers)
if (CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR)
set(spoa_main_project ON)
endif ()
option(spoa_install "Generate library install target" ${spoa_main_project})
option(spoa_build_exe "Build executable" ${spoa_main_project})
option(spoa_build_tests "Build unit tests" ${spoa_main_project})
option(spoa_use_cereal "Use cereal library" OFF)
option(spoa_optimize_for_native "Build with -march=native" ON)
option(spoa_optimize_for_portability "Build with -msse4.1" OFF)
option(spoa_use_simde "Use SIMDe library for porting vectorized code" OFF)
option(spoa_use_simde_nonvec "Use SIMDe library for nonvectorized code" OFF)
option(spoa_use_simde_openmp "Use SIMDe support for OpenMP SIMD" OFF)
option(spoa_generate_dispatch "Use SIMDe to generate x86 dispatch" OFF)
if (NOT spoa_generate_dispatch)
if (spoa_optimize_for_portability)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.1")
elseif (spoa_optimize_for_native)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
endif ()
endif ()
if (spoa_use_simde OR
spoa_use_simde_nonvec OR
spoa_use_simde_openmp OR
spoa_generate_dispatch)
FetchContent_Declare(
simde
GIT_REPOSITORY https://github.com/simd-everywhere/simde
GIT_TAG v0.7.6)
FetchContent_GetProperties(simde)
if (NOT simde_POPULATED)
FetchContent_Populate(simde)
endif ()
add_compile_definitions(SPOA_USE_SIMDE SIMDE_ENABLE_NATIVE_ALIASES)
if (spoa_use_simde_nonvec)
add_compile_definitions(SIMDE_NO_NATIVE)
endif ()
if (spoa_use_simde_openmp)
add_compile_definitions(SIMDE_ENABLE_OPENMP)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp-simd")
endif ()
if (spoa_generate_dispatch)
find_package(CpuFeatures 0.6.0 QUIET)
if (NOT CpuFeatures_FOUND)
if (spoa_install)
message(FATAL_ERROR "Missing package CpuFeatures!")
endif ()
FetchContent_Declare(
cpu_features
GIT_REPOSITORY https://github.com/google/cpu_features
GIT_TAG v0.6.0)
FetchContent_GetProperties(cpu_features)
if (NOT cpu_features_POPULATED)
FetchContent_Populate(cpu_features)
add_subdirectory(
${cpu_features_SOURCE_DIR}
${cpu_features_BINARY_DIR}
EXCLUDE_FROM_ALL)
add_library(CpuFeatures::cpu_features ALIAS cpu_features)
endif ()
endif ()
add_compile_definitions(SPOA_GENERATE_DISPATCH)
endif ()
endif ()
if (spoa_use_cereal)
find_package(cereal 1.3.0 QUIET)
if (NOT cereal_FOUND)
if (spoa_install)
message(FATAL_ERROR "Missing package cereal!")
endif ()
FetchContent_Declare(
cereal
GIT_REPOSITORY https://github.com/USCiLab/cereal
GIT_TAG v1.3.0)
FetchContent_GetProperties(cereal)
if (NOT cereal_POPULATED)
FetchContent_Populate(cereal)
add_subdirectory(
${cereal_SOURCE_DIR}
${cereal_BINARY_DIR}
EXCLUDE_FROM_ALL)
add_library(cereal::cereal ALIAS cereal)
endif ()
endif ()
endif ()
if (spoa_build_tests)
find_package(GTest 1.10.0 QUIET)
if (NOT GTest_FOUND)
FetchContent_Declare(
googletest
GIT_REPOSITORY https://github.com/google/googletest
GIT_TAG release-1.10.0)
FetchContent_GetProperties(googletest)
if (NOT googletest_POPULATED)
FetchContent_Populate(googletest)
add_subdirectory(
${googletest_SOURCE_DIR}
${googletest_BINARY_DIR}
EXCLUDE_FROM_ALL)
add_library(GTest::Main ALIAS gtest_main)
endif ()
endif ()
endif ()
set(SPOA_VERSION "${PROJECT_VERSION}")
configure_file(src/spoa_config.h.in spoa_config.h)
add_library(spoa SHARED
src/alignment_engine.cpp
src/graph.cpp
src/simd_alignment_engine_dispatcher.cpp
src/sisd_alignment_engine.cpp
src/version.cpp)
add_library(spoa::spoa ALIAS spoa)
target_include_directories(spoa PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>
$<BUILD_INTERFACE:${simde_SOURCE_DIR}>
$<INSTALL_INTERFACE:include>)
if (spoa_use_cereal)
target_link_libraries(spoa
cereal::cereal)
target_compile_definitions(spoa PUBLIC SPOA_USE_CEREAL)
endif ()
# if (BUILD_SHARED_LIBS)
set_property(TARGET spoa PROPERTY SOVERSION "7.0.0")
# endif ()
add_library(${PROJECT_NAME}_static STATIC
src/alignment_engine.cpp
src/graph.cpp
src/sisd_alignment_engine.cpp
)
target_include_directories(${PROJECT_NAME}_static PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
/usr/include/cpu_features
$<INSTALL_INTERFACE:include>)
target_link_libraries(${PROJECT_NAME}_static
cereal)
if (spoa_generate_dispatch)
list(APPEND ARCHITECTURES avx2 sse4.1 sse2)
foreach(arch IN LISTS ARCHITECTURES)
add_library(spoa_${arch} OBJECT
src/simd_alignment_engine_dispatch.cpp)
target_include_directories(spoa_${arch} PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
$<BUILD_INTERFACE:${simde_SOURCE_DIR}>
$<INSTALL_INTERFACE:include>)
set_property(TARGET spoa_${arch}
PROPERTY COMPILE_FLAGS "-m${arch}")
if (BUILD_SHARED_LIBS)
set_property(TARGET spoa_${arch}
PROPERTY POSITION_INDEPENDENT_CODE ON)
endif ()
endforeach ()
add_dependencies(spoa
spoa_avx2
spoa_sse4.1
spoa_sse2)
add_dependencies(spoa_static
spoa_avx2
spoa_sse4.1
spoa_sse2)
target_link_libraries(spoa
CpuFeatures::cpu_features)
target_link_libraries(spoa_static
CpuFeatures::cpu_features)
endif ()
if (spoa_install)
configure_package_config_file(
${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
write_basic_package_version_file(
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
COMPATIBILITY SameMajorVersion)
install(
TARGETS spoa
EXPORT ${PROJECT_NAME}Targets
DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(
TARGETS spoa_static
EXPORT ${PROJECT_NAME}Targets
DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(
DIRECTORY include/spoa
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
install(
EXPORT ${PROJECT_NAME}Targets
NAMESPACE ${PROJECT_NAME}::
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
endif ()
if (spoa_build_exe)
add_executable(spoa_exe
src/main.cpp)
target_link_libraries(spoa_exe
spoa
z)
set_property(TARGET spoa_exe PROPERTY OUTPUT_NAME spoa)
install(TARGETS spoa_exe DESTINATION ${CMAKE_INSTALL_BINDIR})
endif ()
if (spoa_build_tests)
set(SPOA_TEST_DATA "${PROJECT_SOURCE_DIR}/test/data/sample.fastq.gz")
configure_file(test/spoa_test_config.h.in spoa_test_config.h)
add_executable(spoa_test
test/spoa_test.cpp)
target_link_libraries(spoa_test
spoa
z
GTest::Main)
target_include_directories(spoa_test PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>)
endif ()
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