FMAlign2/CMakeLists.txt at master · malabz/FMAlign2 · GitHub

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cmake_minimum_required(VERSION 3.15)
project(FMAlign2 VERSION 1.0 LANGUAGES CXX C)

# 设置 C++ 标准
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_C_STANDARD 11)

# 编译选项
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall")

# 包含目录
include_directories(include)

# 源文件
set(SOURCES
    main.cpp
    src/utils.cpp
    src/mem_finder.cpp
    src/sequence_split_align.cpp
    src/ssw.cpp
    src/ssw_cpp.cpp
    src/gsacak.c
)

# 根据操作系统添加不同的源文件
if(WIN32)
    # Windows: 使用 OpenMP
    find_package(OpenMP REQUIRED)
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
else()
    # Linux/Unix: 使用 pthread 和自定义线程池
    list(APPEND SOURCES
        src/thread_pool.cpp
        src/thread_condition.cpp
    )
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
    if(UNIX AND NOT APPLE)
        # Linux 特定: 需要 rt 库
        set(EXTRA_LIBS rt)
    endif()
endif()

# M64 宏定义 (可选，用于大数据)
option(USE_M64 "Use 64-bit integer types" OFF)
if(USE_M64)
    add_definitions(-DM64=1)
endif()

# Debug 宏定义
if(CMAKE_BUILD_TYPE STREQUAL "Debug")
    add_definitions(-DDEBUG=1)
endif()

# 创建可执行文件
add_executable(fmalign2 ${SOURCES})

# 链接库
if(NOT WIN32)
    target_link_libraries(fmalign2 pthread ${EXTRA_LIBS})
endif()

# 静态链接选项 (Linux)
option(STATIC_LINK "Build with static linking" OFF)
if(STATIC_LINK AND UNIX AND NOT APPLE)
    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static -static-libstdc++ -static-libgcc")
    target_link_libraries(fmalign2 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive)
endif()

# Sanitizer 选项 (用于调试)
option(USE_SANITIZER "Build with address and undefined behavior sanitizers" OFF)
if(USE_SANITIZER)
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fsanitize=undefined -fno-omit-frame-pointer")
    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=undefined -fno-omit-frame-pointer")
    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address -fsanitize=undefined")
endif()

# 安装配置
install(TARGETS fmalign2 DESTINATION bin)