CMakeLists.txt

cmake_minimum_required (VERSION 2.8)

IF (MY_COMPILER_OPTION STREQUAL "Intel")
    FIND_PROGRAM(ICPC_PROGRAM icpc ...)
    IF(ICPC_PROGRAM)
        MESSAGE(STATUS "** Compiling with Intel settings **")
        IF(ENV{CXX})
            MESSAGE(WARNING "Overwriting CXX envvar")
        ENDIF()
        SET(ENV{CXX} "${ICPC_PROGRAM}")
        SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -w")
        SET(CMAKE_CXX_FLAGS_DEBUG "-g")
    ELSE()
        MESSAGE(FATAL_ERROR "Intel compiler not found")
    ENDIF()
ENDIF ()

project (skipmer)

## Compiler flags
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fpermissive -w -Wno-deprecated -std=c++14")

set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g")


if (WITH_LARGE_KMERS)
    MESSAGE(STATUS "WITH_LARGE_KMERS")
    add_definitions(-DUSE_LARGE_KMERS=1)
endif()


find_package (Threads)

include(FindOpenMP)
if(OPENMP_FOUND)
    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
endif()

add_definitions(${CMAKE_CXX_FLAGS})

## To move the bins to the final location
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "bin")

find_package(ZLIB REQUIRED)
if (ZLIB_FOUND)
    add_definitions(-DHAVE_ZLIB)
    include_directories(${ZLIB_INCLUDE_DIRS})
endif()

find_package(BZip2 REQUIRED)
if (BZIP2_FOUND)
    add_definitions(-DHAVE_BZIP2)
    include_directories(${BZIP2_INCLUDE_DIRS})
endif()

## Include directories
include_directories("src/")

## Set sources variables

## add executables and respective sources
add_executable(skm-count
               src/skm-count.cc
               src/SkipMer.cc
               src/SkipMer.h
               src/SkipMerSpectrum.cc
               src/SkipMerSpectrum.h)

add_executable(skm-multiway-coverage
               src/skm-multiway-coverage.cc
               src/SkipMer.cc
               src/SkipMer.h
               src/SkipMerPosition.cc
               src/SkipMerPosition.h
               src/SkipMerSpectrum.cc
               src/SkipMerSpectrum.h
               src/SkipMerMultiWayCoverageAnalyser.cc
               src/SkipMerMultiWayCoverageAnalyser.h)

add_executable(skm-align
        src/skm-align.cc
        src/SkipMer.cc
        src/SkipMer.h
        src/SkipMerPosition.cc
        src/SkipMerPosition.h
        src/SkipMerSpectrum.cc
        src/SkipMerSpectrum.h
        src/SkipMerMultiWayCoverageAnalyser.cc
        src/SkipMerMultiWayCoverageAnalyser.h)

add_executable(skm-align2
        src/skm-align2.cc
        src/SkipMer.cc
        src/SkipMer.h
        src/SkipMerPosition.cc
        src/SkipMerPosition.h
        src/SkipMerSpectrum.cc
        src/SkipMerSpectrum.h
        src/SkipMerMultiWayCoverageAnalyser.cc
        src/SkipMerMultiWayCoverageAnalyser.h)


##add_executable(kmatch-dump src/matchdump.cc)

target_link_libraries (skm-count ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${BZIP2_LIBRARIES})
target_link_libraries (skm-multiway-coverage ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${BZIP2_LIBRARIES})
target_link_libraries (skm-align ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${BZIP2_LIBRARIES})
target_link_libraries (skm-align2 ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${BZIP2_LIBRARIES})