CMakeLists.txt

cmake_minimum_required(VERSION 3.4)
include(CheckCXXSourceCompiles)
project(CoCo)

list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.1")

include(GetGitRevisionDescription)
get_git_head_revision(GIT_REFSPEC GIT_SHA1)
add_definitions("-DGIT_SHA1=${GIT_SHA1}")

include_directories(lib/kseq)
include_directories(lib/kmer-cnt)

set(coco_source_files ${CMAKE_CURRENT_SOURCE_DIR}/main.cpp)

list (APPEND KSIZE_DEFAULT_LIST 64)
SET (GATB_CORE_EXCLUDE_TOOLS     1)
SET (GATB_CORE_EXCLUDE_TESTS     1)
SET (GATB_CORE_EXCLUDE_EXAMPLES  1)

add_subdirectory(lib/gatb-core/gatb-core)
add_subdirectory(src)

add_definitions (${gatb-core-flags})
include_directories (${gatb-core-includes})
link_directories (${gatb-core-extra-libraries-path})
set_target_properties(gatbcore-static PROPERTIES COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -w" LINK_FLAGS "${CMAKE_CXX_FLAGS} -w")

add_executable(coco ${coco_source_files} ${coco_header_files})
target_link_libraries (coco ${gatb-core-libraries})

find_package(ZLIB QUIET)
if (ZLIB_FOUND)
    message("-- Found ZLIB")
    set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
    set(OLD_CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES})
    set(OLD_CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES})
    set(CMAKE_REQUIRED_FLAGS -lz)
    set(CMAKE_REQUIRED_INCLUDES ${ZLIB_INCLUDE_DIRS})
    set(CMAKE_REQUIRED_LIBRARIES ${ZLIB_LIBRARIES})
    check_cxx_source_compiles("
        #include <zlib.h>
        int main() { gzFile file; return 0; }"
            HAVE_ZLIB_CHECK)
    set(CMAKE_REQUIRED_FLAGS ${OLD_CMAKE_REQUIRED_FLAGS})
    set(CMAKE_REQUIRED_INCLUDES ${OLD_CMAKE_REQUIRED_INCLUDES})
    set(CMAKE_REQUIRED_LIBRARIES ${OLD_CMAKE_REQUIRED_LIBRARIES})
    if(HAVE_ZLIB_CHECK)
        message("-- ZLIB works")
        target_include_directories(coco PUBLIC ${ZLIB_INCLUDE_DIRS})
        target_compile_definitions(coco PUBLIC -DHAVE_ZLIB=1)
        target_link_libraries(coco ${ZLIB_LIBRARIES})
    else ()
        message("-- ZLIB does not work")
    endif()
else ()
    message("-- Could not find ZLIB")
endif ()

find_package(BZip2 QUIET)
if (BZIP2_FOUND)
    message("-- Found BZLIB")
    set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
    set(OLD_CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES})
    set(OLD_CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES})
    set(CMAKE_REQUIRED_FLAGS -lbz2)
    set(CMAKE_REQUIRED_INCLUDES ${BZIP_INCLUDE_DIRS})
    set(CMAKE_REQUIRED_LIBRARIES ${BZIP2_LIBRARIES})
    check_cxx_source_compiles("
        #include <bzlib.h>
        int main() { bz_stream stream; return 0; }"
            HAVE_BZLIB_CHECK)
    set(CMAKE_REQUIRED_FLAGS ${OLD_CMAKE_REQUIRED_FLAGS})
    set(CMAKE_REQUIRED_INCLUDES ${OLD_CMAKE_REQUIRED_INCLUDES})
    set(CMAKE_REQUIRED_LIBRARIES ${OLD_CMAKE_REQUIRED_LIBRARIES})
    if(HAVE_BZLIB_CHECK)
        message("-- BZLIB works")
        target_include_directories(coco PUBLIC ${BZIP_INCLUDE_DIRS})
        target_compile_definitions(coco PUBLIC -DHAVE_BZLIB=1)
        target_link_libraries(coco ${BZIP2_LIBRARIES})
    else ()
        message("-- BZLIB does not work")
    endif()
else ()
    message("-- Could not find BZLIB")
endif ()