CMakeLists.txt

cmake_minimum_required(VERSION 2.8.12)

project(splitcode)

include(GNUInstallDirs)

set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
set(CMAKE_CXX_FLAGS_PROFILE "-g")

if(NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE "Release")
endif()

if(${CMAKE_VERSION} VERSION_LESS 3.1)
    add_compile_options(-std=c++11)
else()
    set(CMAKE_CXX_STANDARD 11)
    set(CMAKE_CXX_STANDARD_REQUIRED ON)
    set(CMAKE_CXX_EXTENSIONS OFF)
endif()

if(LINK MATCHES static)
    message("static build")
ELSE(LINK MATCHES shared)
    message("shared build")
ENDIF(LINK MATCHES static)

set(USE_HTSLIB "ON")
if (NO_HTSLIB)
    set(USE_HTSLIB OFF)
endif()

if(EMSCRIPTEN_BUILD)
    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -s USE_ZLIB=1")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -s USE_ZLIB=1")
    set(USE_HTSLIB OFF)
endif()

add_subdirectory(src)

if (BUILD_FUNCTESTING)
    add_subdirectory(func_tests)
    message("Functional testing enabled.")
    add_custom_target(test
    COMMAND /bin/bash ./func_tests/runtests.sh
    DEPENDS ./src/splitcode
    )
endif(BUILD_FUNCTESTING)

include(ExternalProject)



if (ZLIBNG)
    message("zlib-ng enabled.")
    ExternalProject_Add(zlib-ng
    PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng
    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
    BUILD_IN_SOURCE 1
    CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX}
    BUILD_COMMAND cd zlib-ng && make
    INSTALL_COMMAND ""
    )
endif(ZLIBNG)


if (USE_HTSLIB)
    message("using htslib")
    ExternalProject_Add(htslib
    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
    BUILD_IN_SOURCE 1
    CONFIGURE_COMMAND ""
    BUILD_COMMAND make lib-static
    INSTALL_COMMAND ""
    )
else()
    set(NO_HTSLIB "ON")
    add_compile_definitions("NO_HTSLIB=ON")
    message("not using htslib")
endif()