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CC=g++
EXEC=mapsembler
#CFLAGS= -O4 -lz --std=gnu++0x
#CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER
CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
#CFLAGS= -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER
#CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER
SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp Extension.cpp Extension_Bank.cpp Starter.cpp commons.cpp read_coherence_mapsembler/libchash.cpp read_coherence_mapsembler/couple.cpp read_coherence_mapsembler/misc_tools.cpp read_coherence_mapsembler/read_groups.cpp read_coherence_mapsembler/consensus_common.cpp read_coherence_mapsembler/list.cpp read_coherence_mapsembler/read_coherence.cpp read_coherence_mapsembler/interface_libchash.cpp BooleanVector.cpp Starter_Bank.cpp IterativeExtensions.cpp Fragment_Bank.cpp Fragment.cpp GraphOutput.cpp
OBJ= $(SRC:.cpp=.o)
all: $(EXEC)
ifeq ($(prof),1)
CFLAGS+=-O3 -pg
endif
ifeq ($(deb),1)
CFLAGS+=-O0 -DASSERTS -g
endif
k := 0$(k) # dummy k if not specified
K_BELOW_32 := $(shell echo $(k)\<=32 | bc)
K_BELOW_64 := $(shell echo $(k)\<=64 | bc)
ARCH := $(shell getconf LONG_BIT) # detects sizeof(int)
USING_UINT128 := 0
ifeq ($(K_BELOW_32),0)
# use uint128 when k<=64 and 64-bit architecture
ifeq ($(K_BELOW_64),1)
ifeq ($ARCH),64)
CFLAGS += -Dkmer_type=__uint128_t
USING_UINT128 := 1
endif
endif
# use a bigint library otherwise
ifeq ($(USING_UINT128),0)
ttmath := 1
endif
endif
# ttmath is used when you type "make k=[kmer size]" with a kmer size longer than supported integer type,
# or when typing "make k=[anything] ttmath=1"
ifeq ($(ttmath),1)
KMER_PRECISION := $(shell echo \($(k)+15\)/16 | bc)
CFLAGS += -D_ttmath -DKMER_PRECISION=$(KMER_PRECISION)
endif
all: $(EXEC)
mapsembler: $(OBJ) $(OBJ2) mapsembler.cpp
#mapsembler: $(OBJ) $(OBJ2) test.cpp
$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
%.o: %.cpp %.h
$(CC) -lz -o $@ -c $< $(CFLAGS)
CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
#%.o: %.c %.h
# $(CC) -o $@ -c $< $(CFLAGS)
clean:
rm -rf *.o ../minia/*.o read_coherence_mapsembler/*.o
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