CMakeLists.txt

cmake_minimum_required(VERSION 2.8...3.23)
project(qbcf)

set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -pthread -std=c++11")

set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin")

find_path(HTS_INCLUDE_DIRS htslib/bgzf.h ../htslib/bgzf.h HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/ ../htslib)
if(NOT HTS_INCLUDE_DIRS )
    message(FATAL_ERROR "libhts HTS_INCLUDE_DIRS not found")
endif()

message(STATUS ${HTS_INCLUDE_DIRS})

find_library(HTS_LIBRARIES libhts.a HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/ ../htslib/)
if(NOT HTS_LIBRARIES)
    message(FATAL_ERROR "libhts HTS_LIBRARIES not found")
endif()

message(STATUS ${HTS_LIBRARIES})

find_path(QGEN_INCLUDE_DIRS qgenlib/qgen_error.h  HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/ ../qgenlib)
if(NOT QGEN_INCLUDE_DIRS )
    message(FATAL_ERROR "libqgen QGEN_INCLUDE_DIRS not found")
endif()

message(STATUS ${QGEN_INCLUDE_DIRS})

find_library(QGEN_LIBRARIES libqgen.a  HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/ ../qgenlib/lib/)
if(NOT QGEN_LIBRARIES)
    message(FATAL_ERROR "libqgen QGEN_LIBRARIES not found")
endif()

message(STATUS ${QGEN_LIBRARIES})

include_directories(${HTS_INCLUDE_DIRS} ${QGEN_INCLUDE_DIRS})

set(SOURCE_FILES
    nuclear_pedigree.h nuclear_pedigree.cpp
    sex_ploidy_map.h sex_ploidy_map.cpp
    bcf_utils.h bcf_utils.cpp
    qbcf_cally.cpp
    qbcf_test_qgenlib.cpp
    qbcf.h qbcf.cpp
    )

SET(APP_EXE qbcf)

#find_package(OpenMP REQUIRED)
ADD_EXECUTABLE(${APP_EXE} ${SOURCE_FILES})

find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT ZLIB)
    message(FATAL_ERROR "libz library not found")
endif()

find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT CURLLIB)
    message(FATAL_ERROR "libcurl library not found")
endif()

find_package (BZip2)
if (NOT BZIP2_FOUND)
    message(FATAL_ERROR "libbz2 library not found")
else()
    include_directories(${BZIP2_INCLUDE_DIRS})
    set(BZIP2 ${BZIP2_LIBRARIES})
endif()

find_library(LZMA lzma HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT LZMA)
    message(WARNING "liblzma library not found, if you specified --disable-lzma when compiling libhts, please ignore this warning")
    set(LZMA "")
else()
    set(LZMA ${LZMA_LIBRARIES})
endif()

find_library(CRYPTOLIB crypto HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT CRYPTOLIB)
    message(FATAL_ERROR "libcrypto library not found")
endif()

TARGET_LINK_LIBRARIES(${APP_EXE} PRIVATE ${QGEN_LIBRARIES} ${HTS_LIBRARIES} ${ZLIB} ${LZMA} ${BZIP2} ${CURLLIB} ${CRYPTOLIB} "${OpenMP_CXX_FLAGS}")
target_compile_options(${APP_EXE} PRIVATE "${OpenMP_CXX_FLAGS}")


install(TARGETS ${APP_EXE} RUNTIME DESTINATION bin)