CMakeLists.txt

cmake_minimum_required(VERSION 3.11 FATAL_ERROR)
project(mashmap VERSION 3.0.0)

include(GNUInstallDirs)
include(CheckCXXCompilerFlag)

set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)  # Falling back to different standard it not allowed.
set(CMAKE_CXX_EXTENSIONS OFF)  # Make sure no compiler-specific features are used.
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)


#set(CMAKE_BUILD_TYPE Release)
if(NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE Release CACHE STRING
            "Choose the type of build, options are: Release Debug Generic." FORCE)
endif()

message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")

option(SKIP_VERSION_FILE "Do not create src/mashmap_git_version.hpp" OFF)
option(OPTIMIZE_FOR_NATIVE "Build with -march=native" ON)
option(LARGE_CONTIG "Use 64-bit integers instead of 32 bit for sequence coordinates" OFF)
if (LARGE_CONTIG)
  add_definitions(-DLARGE_CONTIG)
endif()
option(USE_HTSLIB "Compile with htslib for --targetPrefix and --targetList" OFF)
if (USE_HTSLIB)
  add_definitions(-DUSE_HTSLIB)
  find_package(PkgConfig)
  pkg_check_modules(HTSLIB REQUIRED IMPORTED_TARGET htslib)
endif()
option(PROFILE             "Prevent inlining and add debug symbols" OFF)

if (${CMAKE_BUILD_TYPE} MATCHES Release)
    if (OPTIMIZE_FOR_NATIVE)
      set(EXTRA_FLAGS "${EXTRA_FLAGS} -march=native")
    endif ()
    if (PROFILE)
      set(EXTRA_FLAGS "${EXTRA_FLAGS} -g -fno-inline")
    endif()
endif ()

if (${CMAKE_BUILD_TYPE} MATCHES Debug)
    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O -g")
    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O -g")
    add_compile_options(-fsanitize=address)
    add_link_options(-fsanitize=address)
else()
    # Use all standard-compliant optimizations - always add these:
    set (CMAKE_C_FLAGS "${OpenMP_C_FLAGS} ${PIC_FLAG} ${EXTRA_FLAGS}")
    set (CMAKE_CXX_FLAGS "${OpenMP_CXX_FLAGS} ${PIC_FLAG} ${EXTRA_FLAGS}")
endif ()

set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)

add_compile_options(-Wfatal-errors)

#include(FetchContent)
#FetchContent_Declare(
    #assert
    #URL https://github.com/jeremy-rifkin/libassert/archive/refs/tags/v1.1.tar.gz
#)
#FetchContent_MakeAvailable(assert)

add_executable(mashmap
  src/common/utils.cpp
  src/map/mash_map.cpp) 

add_executable(mashmap-align
  src/common/utils.cpp
  src/align/align.cpp) 

target_include_directories(mashmap PRIVATE
  src
  src/common
)

target_include_directories(mashmap-align PRIVATE
  src
  src/common
)

if (USE_HTSLIB)
  target_link_libraries(mashmap PkgConfig::HTSLIB)
  target_link_libraries(mashmap-align PkgConfig::HTSLIB)
endif()

target_link_libraries(mashmap
  gsl
  gslcblas
  m
  pthread
  #rt
  z
  #assert
)

target_link_libraries(mashmap-align
  gsl
  gslcblas
  m
  pthread
  #rt
  z
  #assert
)

install(TARGETS mashmap DESTINATION bin)
install(TARGETS mashmap-align DESTINATION bin)

# version stuff
if (NOT SKIP_VERSION_FILE)
  file(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/include)
  execute_process(COMMAND bash ${CMAKE_SOURCE_DIR}/scripts/generate_git_version.sh ${CMAKE_SOURCE_DIR}/src)
endif ()