CMakeLists.txt

cmake_minimum_required(VERSION 3.5)
project(SSHASH)

set(CMAKE_CXX_STANDARD 17)
if (NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE "Release")
endif ()

if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
endif ()

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

set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})

MESSAGE(STATUS "Compiling for processor: " ${CMAKE_HOST_SYSTEM_PROCESSOR})

if (UNIX AND (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64"))
  MESSAGE(STATUS "Compiling with flags: -march=native -mbmi2 -msse4.2")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
  # Flags for PTHash:
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mbmi2 -msse4.2") # for hardware popcount and pdep
endif()

if (SSHASH_USE_MAX_KMER_LENGTH_63)
  MESSAGE(STATUS "SSHash uses a maximum kmer length of 63")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSSHASH_USE_MAX_KMER_LENGTH_63")
else()
  MESSAGE(STATUS "SSHash uses a maximum kmer length of 31")
endif()

if (SSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING)
  MESSAGE(STATUS "SSHash maps {'A','a'}->0, {'C','c'}->1, {'G','g'}->2, and {'T','t'}->3")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING")
else()
  MESSAGE(STATUS "SSHash maps {'A','a'}->0, {'C','c'}->1, {'T','t'}->2, and {'G','g'}->3")
endif()

if (UNIX)

  MESSAGE(STATUS "Compiling with flags: -std=c++17 -O3 -ggdb -pthread -Wall -Wextra -Wno-missing-braces -Wno-unknown-attributes -Wno-unused-function")

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ggdb")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-missing-braces -Wno-unknown-attributes -Wno-unused-function")

  # Flags for PTHash:
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread") # for multi-threading

  if (SSHASH_USE_SANITIZERS)
    MESSAGE(STATUS "Using sanitizers. Compiling with flags: -fsanitize=address -fno-omit-frame-pointer")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fno-omit-frame-pointer")
  endif()

endif()

include_directories(.) # all include paths relative to parent directory
include_directories(external/pthash)
include_directories(external/pthash/external/essentials/include)

set(Z_LIB_SOURCES
  include/gz/zip_stream.cpp
)

set(SSHASH_SOURCES
  include/dictionary.cpp
  include/info.cpp
  include/dump.cpp
  include/statistics.cpp
  include/builder/build.cpp
)

# Create a static lib
add_library(sshash_static STATIC
  ${Z_LIB_SOURCES}
  ${SSHASH_SOURCES}
)

add_executable(sshash src/sshash.cpp)
target_link_libraries(sshash
  sshash_static
  z
)

# tests
add_executable(test_alphabet test/test_alphabet.cpp)
target_link_libraries(test_alphabet
  sshash_static
)