Makefile

SDSL_DIR=../sdsl-lite
include $(SDSL_DIR)/Make.helper

BUILD_BIN=bin
BUILD_LIB=lib
BUILD_OBJ=obj
SOURCE_DIR=src

# Multithreading with OpenMP.
PARALLEL_FLAGS=-fopenmp -pthread
LIBS=-L$(LIB_DIR) -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64

# Apple Clang does not support OpenMP directly, so we need special handling.
ifeq ($(shell uname -s), Darwin)
    # The compiler complains about -fopenmp instead of missing input.
    ifeq ($(strip $(shell $(MY_CXX) -fopenmp /dev/null -o/dev/null 2>&1 | grep fopenmp | wc -l)), 1)
        $(info The compiler is Apple Clang that needs libomp for OpenMP support.)

        # The compiler only needs to do the preprocessing.
        PARALLEL_FLAGS = -Xpreprocessor -fopenmp -pthread

        # Find libomp installed by Homebrew or MacPorts.
        ifeq ($(shell if [ -e $(HOMEBREW_PREFIX)/include/omp.h ]; then echo 1; else echo 0; fi), 1)
            $(info Found libomp installed by Homebrew and linked to $(HOMEBREW_PREFIX).)
            PARALLEL_FLAGS += -I$(HOMEBREW_PREFIX)/include
            LIBS += -L$(HOMEBREW_PREFIX)/lib
        else ifeq ($(shell if [ -d $(HOMEBREW_PREFIX)/opt/libomp/include ]; then echo 1; else echo 0; fi), 1)
            $(info Found a keg-only libomp installed by Homebrew at $(HOMEBREW_PREFIX)/opt/libomp.)
            PARALLEL_FLAGS += -I$(HOMEBREW_PREFIX)/opt/libomp/include
            LIBS += -L$(HOMEBREW_PREFIX)/opt/libomp/lib
        else ifeq ($(shell if [ -d /opt/local/lib/libomp ]; then echo 1; else echo 0; fi), 1)
            $(info Found libomp installed by MacPorts at /opt/local.)
            PARALLEL_FLAGS += -I/opt/local/include/libomp
            LIBS += -L/opt/local/lib/libomp
        else
            $(error Could not find libomp. Please install it using Homebrew or MacPorts.)
        endif

        # We also need to link it.
        LIBS += -lomp
    endif
endif

CXX_FLAGS=$(MY_CXX_FLAGS) $(PARALLEL_FLAGS) $(MY_CXX_OPT_FLAGS) -Iinclude -I$(INC_DIR)

HEADERS=$(wildcard include/gbwtgraph/*.h)
LIBOBJS=$(addprefix $(BUILD_OBJ)/,algorithms.o cached_gbwtgraph.o gbwtgraph.o gbz.o gfa.o internal.o minimizer.o path_cover.o subgraph.o utils.o)
LIBRARY=$(BUILD_LIB)/libgbwtgraph.a

PROGRAMS=$(addprefix $(BUILD_BIN)/,gfa2gbwt gbz_extract gbz_stats kmer_freq subgraph_query)
OBSOLETE=gfa2gbwt

.PHONY: all clean directories test
all: directories $(LIBRARY) $(PROGRAMS)

directories: $(BUILD_BIN) $(BUILD_LIB) $(BUILD_OBJ)

$(BUILD_BIN):
	mkdir -p $@

$(BUILD_LIB):
	mkdir -p $@

$(BUILD_OBJ):
	mkdir -p $@

$(BUILD_OBJ)/%.o:$(SOURCE_DIR)/%.cpp $(HEADERS)
	$(MY_CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXX_FLAGS) -c -o $@ $<

$(LIBRARY):$(LIBOBJS)
	ar rcs $@ $(LIBOBJS)

$(BUILD_BIN)/%:$(BUILD_OBJ)/%.o $(LIBRARY)
	$(MY_CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(CXX_FLAGS) -o $@ $< $(LIBRARY) $(LIBS)

test:$(LIBRARY)
	cd tests && $(MAKE) test

clean:
	rm -rf $(BUILD_BIN) $(BUILD_LIB) $(BUILD_OBJ)
	rm -f *.o *.a $(OBSOLETE)
	cd tests && $(MAKE) clean