CMakeListsKMC.txt.in

cmake_minimum_required(VERSION 2.8.2)

project(KMC)


if(APPLE)
string(APPEND CMAKE_CXX_FLAGS " \
    -Wall -O3 -m64 \
    -pthread -std=c++11 \
")
elseif(UNIX)
string(APPEND CMAKE_CXX_FLAGS " \
    -Wall -O3 -m64 -Wl,--whole-archive \
    -pthread -Wl,--no-whole-archive -std=c++11 \
")
endif()

if(@BUILD_STATIC@)
string(APPEND CMAKE_CXX_FLAGS " -static ")
endif()

set(KMC_MAIN_DIR @KMC_MAIN_DIR@)

file(GLOB KMC_files
#${KMC_MAIN_DIR}/kmer_counter.cpp
${KMC_MAIN_DIR}/mmer.cpp
${KMC_MAIN_DIR}/mem_disk_file.cpp
${KMC_MAIN_DIR}/rev_byte.cpp
${KMC_MAIN_DIR}/bkb_writer.cpp
${KMC_MAIN_DIR}/cpu_info.cpp
${KMC_MAIN_DIR}/bkb_reader.cpp
${KMC_MAIN_DIR}/fastq_reader.cpp
${KMC_MAIN_DIR}/timer.cpp
${KMC_MAIN_DIR}/develop.cpp
${KMC_MAIN_DIR}/kb_completer.cpp
${KMC_MAIN_DIR}/kb_storer.cpp
${KMC_MAIN_DIR}/kmer.cpp
${KMC_MAIN_DIR}/splitter.cpp
${KMC_MAIN_DIR}/kb_collector.cpp
${KMC_MAIN_DIR}/../kmc_api/mmer.cpp
${KMC_MAIN_DIR}/../kmc_api/kmc_file.cpp
${KMC_MAIN_DIR}/../kmc_api/kmer_api.cpp
)

file(GLOB RADULS_files
${KMC_MAIN_DIR}/raduls_sse2.cpp
${KMC_MAIN_DIR}/raduls_sse41.cpp
${KMC_MAIN_DIR}/raduls_avx2.cpp
${KMC_MAIN_DIR}/raduls_avx.cpp
)

set_source_files_properties(${KMC_MAIN_DIR}/raduls_sse2.cpp
    PROPERTIES COMPILE_FLAGS "-msse2")
set_source_files_properties(${KMC_MAIN_DIR}/raduls_sse41.cpp
    PROPERTIES COMPILE_FLAGS "-msse4.1")
set_source_files_properties(${KMC_MAIN_DIR}/raduls_avx.cpp
    PROPERTIES COMPILE_FLAGS "-mavx")
set_source_files_properties(${KMC_MAIN_DIR}/raduls_avx2.cpp
    PROPERTIES COMPILE_FLAGS "-mavx2 -mfma")

add_library(KMCcore STATIC
    ${KMC_files}
    ${RADULS_files}
)

target_link_libraries(KMCcore
)

add_custom_target(link_target ALL
    COMMAND ${CMAKE_COMMAND} -E
        create_symlink "libKMCcore.a" "libKMC.a"
    DEPENDS KMCcore
)


if(@BUILD_KMC@)

add_executable(kmc
    ${KMC_MAIN_DIR}/kmer_counter.cpp
)

target_link_libraries(kmc
    KMCcore
    -lz -lbz2 -lpthread
)

endif()