CMakeLists.txt

cmake_minimum_required (VERSION 3.8)

project(segalign LANGUAGES CXX CUDA)
project(segalign_repeat_masker LANGUAGES CXX CUDA)

set(CMAKE_CUDA_COMPILER nvcc)
find_package(CUDA 9.0 REQUIRED)

set(CMAKE_CUDA_COMPILER_ENV_VAR "CUDACXX")
set(CMAKE_CUDA_HOST_COMPILER_ENV_VAR "CUDAHOSTCXX")

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O4 -std=c++11 -l c -lboost_program_options")
set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -arch=sm_52")

include(${TBB_ROOT}/cmake/TBBBuild.cmake)
tbb_build(TBB_ROOT ${TBB_ROOT} CONFIG_DIR TBB_DIR MAKE_ARGS tbb_cpf=1)
find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb_preview)

find_package(ZLIB REQUIRED)
find_path(ZLIB_INCLUDE_DIR zlib.h)
include_directories(${ZLIB_INCLUDE_DIR})

find_package(Boost COMPONENTS program_options REQUIRED)
include_directories(${Boost_INCLUDE_DIRS})

add_executable(segalign
    common/DRAM.cpp
    common/ntcoding.cpp
    common/seed_filter_interface.cu
    common/seed_pos_table.cu
    src/seed_filter.cu
    src/seeder.cpp
    src/segment_printer.cpp
    src/main.cpp
    )

add_executable(segalign_repeat_masker
    common/DRAM.cpp
    common/ntcoding.cpp
    common/seed_filter_interface.cu
    common/seed_pos_table.cu
    repeat_masker_src/seed_filter.cu
    repeat_masker_src/seeder.cpp
    repeat_masker_src/segment_printer.cpp
    repeat_masker_src/main.cpp
    )

set(LIBS rt stdc++ ${TBB_IMPORTED_TARGETS} ${Boost_LIBRARIES} ${CUDA_LIBRARIES} ${ZLIB_LIBRARIES})

set_target_properties(
    segalign 
    segalign_repeat_masker
    PROPERTIES 
      CUDA_SEPARABLE_COMPILATION ON
      CUDA_STANDARD 11
      )

target_compile_options(segalign PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
target_compile_options(segalign_repeat_masker PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)

target_link_libraries(segalign PRIVATE ${LIBS})
target_link_libraries(segalign_repeat_masker PRIVATE ${LIBS})

target_include_directories(segalign PRIVATE ${PROJECT_SOURCE_DIR}/common/ ${PROJECT_SOURCE_DIR}/src/)
target_include_directories(segalign_repeat_masker PRIVATE ${PROJECT_SOURCE_DIR}/common/ ${PROJECT_SOURCE_DIR}/repeat_masker_src/)