cmake_minimum_required(VERSION 3.21)

project(

AWFMIndex

HOMEPAGE_URL https://github.com/TravisWheelerLab/AvxWindowFmIndex

LANGUAGES C # Specify C language explicitly

)

set(CMAKE_C_STANDARD 17)

set(CMAKE_POSITION_INDEPENDENT_CODE ON)

#add support for OpenMP

find_package(OpenMP REQUIRED)

if(OpenMP_FOUND)

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")

endif()

set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY build)

set(CMAKE_LIBRARY_OUTPUT_DIRECTORY build)

#PUBLIC_H_FILES is missing divsufsort64.h, because it doesn't exist until after divsufsort is built

set(

PUBLIC_H_FILES

src/AwFmIndex.h

lib/FastaVector/src/FastaVector.h

lib/FastaVector/src/FastaVectorMetadataVector.h

lib/FastaVector/src/FastaVectorString.h

)

set(

H_FILES

src/AwFmCreate.h

src/AwFmFile.h

src/AwFmIndex.h

src/AwFmIndexStruct.h

src/AwFmKmerTable.h

src/AwFmLetter.h

src/AwFmOccurrence.h

src/AwFmParallelSearch.h

src/AwFmSearch.h

src/AwFmSimdConfig.h

src/AwFmSuffixArray.h

)

set(

C_FILES

src/AwFmCreate.c

src/AwFmFile.c

src/AwFmIndexStruct.c

src/AwFmKmerTable.c

src/AwFmLetter.c

src/AwFmOccurrence.c

src/AwFmParallelSearch.c

src/AwFmSearch.c

src/AwFmSimdConfig.c

src/AwFmSuffixArray.c

)

add_library(

awfmindex_static STATIC

${C_FILES}

)

add_library(

awfmindex SHARED

${C_FILES}

)

# Set public headers for awfmindex_static

set_target_properties(

awfmindex_static

PROPERTIES

PUBLIC_HEADER "${PUBLIC_H_FILES}"

)

# Set public headers for awfmindex

set_target_properties(

awfmindex

PROPERTIES

PUBLIC_HEADER "${PUBLIC_H_FILES}"

)

add_custom_target(

copy_headers

COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_CURRENT_BINARY_DIR}/include/AWFMIndex

)

#copy the libdivsufsort and fastavector static libs to the build director

add_custom_command(

TARGET awfmindex_static

POST_BUILD

COMMAND ${CMAKE_COMMAND} -E copy

$<TARGET_FILE:divsufsort64>

$<TARGET_FILE_DIR:awfmindex_static>

)

add_custom_command(

TARGET awfmindex_static

POST_BUILD

COMMAND ${CMAKE_COMMAND} -E copy

$<TARGET_FILE:divsufsort64>

$<TARGET_FILE:fastavector_static>

$<TARGET_FILE_DIR:awfmindex_static>

)

# Set common compiler options

target_compile_options(

awfmindex_static

PRIVATE

-mtune=native

-march=native

-Wall

-Wextra

-O3

-fPIC

-lgomp

${OpenMP_C_FLAGS}

)

target_compile_options(

awfmindex

PRIVATE

-mtune=native

-march=native

-Wall

-Wextra

-O3

-fPIC

-lgomp

${OpenMP_C_FLAGS}

)

# Check if the target architecture is x86_64 (Intel) or aarch64 (ARM)

if(CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64")

# Check if the compiler supports AVX2

include(CheckCCompilerFlag)

CHECK_C_COMPILER_FLAG("-mavx2" COMPILER_SUPPORTS_AVX2)

if(COMPILER_SUPPORTS_AVX2)

# Set AVX2 flags for x86_64 (Intel)

target_compile_options(awfmindex_static PRIVATE -mavx2)

target_compile_options(awfmindex PRIVATE -mavx2)

endif()

elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64")

# Set NEON flags for ARM

target_compile_options(awfmindex_static PRIVATE -march=armv8-a+simd)

target_compile_options(awfmindex PRIVATE -march=armv8-a+simd)

endif()

install(

TARGETS awfmindex awfmindex_static

)

# ------------

# Dependencies

# ------------

set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries" FORCE)

set(CMAKE_BUILD_TYPE "Release")

add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/lib/)

# Custom target for building submodules

add_custom_target(build_submodule

COMMENT "Building submodules"

)

# Custom command to copy public headers after building submodules

foreach(HEADER ${PUBLIC_H_FILES})

add_custom_command(

TARGET build_submodule # Add dependency on build_submodule

COMMAND ${CMAKE_COMMAND} -E copy

${CMAKE_CURRENT_SOURCE_DIR}/${HEADER}

${CMAKE_CURRENT_BINARY_DIR}/build

)

endforeach()

add_dependencies(awfmindex_static build_submodule)

add_dependencies(awfmindex_static copy_headers)

# FastaVector

target_include_directories(

awfmindex_static PRIVATE

${CMAKE_CURRENT_SOURCE_DIR}/lib/FastaVector/src/

)

target_include_directories(

awfmindex PRIVATE

${CMAKE_CURRENT_SOURCE_DIR}/lib/FastaVector/src/

)

target_link_libraries(awfmindex_static PRIVATE fastavector_static)

target_link_libraries(awfmindex PRIVATE fastavector)

# libdivsufsort

target_include_directories(

awfmindex PRIVATE

${CMAKE_CURRENT_SOURCE_DIR}/lib/libdivsufsort/include/

)

target_include_directories(

awfmindex_static PRIVATE

${CMAKE_CURRENT_SOURCE_DIR}/lib/libdivsufsort/include/

)

target_link_libraries(awfmindex_static PRIVATE divsufsort64)

target_link_libraries(awfmindex PRIVATE divsufsort64)

# Custom target for building submodules

add_custom_target(build_divsufsort

COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/lib/

COMMENT "Building submodule"

)

set_target_properties(build_divsufsort PROPERTIES POSITION_INDEPENDENT_CODE ON)

# Custom command to move the divsufsort64.h file after the end of the build

add_custom_command(

TARGET awfmindex_static POST_BUILD # Add dependency on build_submodule

COMMAND ${CMAKE_COMMAND} -E copy

${CMAKE_CURRENT_BINARY_DIR}/lib/libdivsufsort/include/divsufsort64.h

${CMAKE_CURRENT_BINARY_DIR}/build/

)

add_custom_command(

TARGET awfmindex_static POST_BUILD # Add dependency on build_submodule

COMMAND ${CMAKE_COMMAND} -E copy

${CMAKE_CURRENT_BINARY_DIR}/lib/libdivsufsort/lib/build/libdivsufsort64.a

${CMAKE_CURRENT_BINARY_DIR}/build/

)

# Add a dependency on build_submodule

add_dependencies(awfmindex_static build_divsufsort)