cmake_minimum_required(VERSION 2.8)
project(TN93)

#-------------------------------------------------------------------------------
# default installation prefix
#-------------------------------------------------------------------------------
set(INSTALL_PREFIX /usr/local CACHE PATH "Installation prefix")
set(CMAKE_INSTALL_PREFIX ${INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)

set(CMAKE_CONFIGURATION_TYPES Release)

# SET VERSION FROM FILE
file (STRINGS "VERSION.txt" VERSION_NUMBER)
add_definitions (-DVERSION_NUMBER=\"${VERSION_NUMBER}\")

include_directories(
    src/
)

add_executable(
    tn93
    src/TN93.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
    src/argparse.cpp
)

add_executable(
    tn93-cluster
    src/cluster.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
    src/argparse_cluster.cpp
)


add_executable(
    seqcoverage
    src/charfreqs.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
    src/argparse_cf.cpp
)

add_executable(
    readreduce
    src/read_reducer.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
    src/argparse_merge.cpp
)

add_executable(
    nucfreqsfasta
    src/nuc_freqs_from_fasta.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
)

add_executable(
    ShortestPathTN93
    src/ShortestPathTN93.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
)

add_executable(
    selectreads
    src/trim_reads.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
    src/argparse_trim.cpp
)

add_executable(
    validate_fasta
    src/validate_fasta.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
)

add_executable(
    fasta_diff
    src/fasta_diff.cpp
    src/stringBuffer.cc
    src/tn93_shared.cc
    src/argparse_fasta_diff.cpp
)

#set(DEFAULT_COMPILE_FLAGS "-O3 -march=native -g -mveclibabi=svml -mstringop-strategy=vector_loop -Wa,-q")
set(DEFAULT_COMPILE_FLAGS "-O3 -std=c++11 -march=native -funroll-loops")

set(DEFAULT_LINK_FLAGS "${DEFAULT_COMPILE_FLAGS}")

find_package(OpenMP)

if (${OPENMP_FOUND})
	set_target_properties(
		tn93
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
	)
	set_target_properties(
		tn93-cluster
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
	)
	set_target_properties(
		selectreads
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
	)
	set_target_properties(
		seqcoverage
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
	)
	set_target_properties(
		ShortestPathTN93
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
    )
	set_target_properties(
		readreduce
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
    )

	set_target_properties(
		fasta_diff
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS} "
    )

endif (${OPENMP_FOUND})

	set_target_properties(
		fasta_diff
		PROPERTIES
		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -std=c++14 "
   )

install(
    TARGETS tn93
	RUNTIME DESTINATION bin
	OPTIONAL
)

install(
    TARGETS tn93-cluster
	RUNTIME DESTINATION bin
	OPTIONAL
)

install(
    TARGETS selectreads
	RUNTIME DESTINATION bin
	OPTIONAL
)

install(
    TARGETS seqcoverage
	RUNTIME DESTINATION bin
	OPTIONAL
)

install(
    TARGETS readreduce
	RUNTIME DESTINATION bin
	OPTIONAL
)

install(
    TARGETS fasta_diff
	RUNTIME DESTINATION bin
	OPTIONAL
)

#add_custom_target(TN93
#  DEPENDS tn93
#)


install(
    TARGETS ShortestPathTN93
	RUNTIME DESTINATION bin
	OPTIONAL
)

add_custom_target(TN93SP
	DEPENDS ShortestPathTN93
)


#add_custom_target(SEQCOVERAGE
#  DEPENDS seqcoverage
#)

install(
    TARGETS nucfreqsfasta
	RUNTIME DESTINATION bin
	OPTIONAL
)

add_custom_target(NF
	DEPENDS nucfreqsfasta
)