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|
CXX=g++
EXEC=mapsembler_extend
#CFLAGS= -O4 -lz
#CFLAGS= -g -lz
#CFLAGS= -g -lz
CFLAGS= -O3 -lz
ifeq "$(CXX)" "g++"
empty:=
space:= $(empty) $(empty)
GCCVERSIONSTRING := $(shell expr `$(CXX) -dumpversion`)
#Create version number without "."
GCCVERSION := $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f1 -d.)
GCCVERSION += $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f2 -d.)
GCCVERSION += $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f3 -d.)
# Make sure the version number has at least 3 decimals
GCCVERSION += 00
# Remove spaces from the version number
GCCVERSION := $(subst $(space),$(empty),$(GCCVERSION))
# Crop the version number to 3 decimals.
GCCVERSION := $(shell expr `echo $(GCCVERSION)` | cut -b1-3)
INT_GCC_VERSION := $(shell expr `echo $(GCCVERSION)` \>= 470)
ifeq "$(INT_GCC_VERSION)" "1"
CFLAGS += --std=c++11 -DMINIA_IS_IN_PARENT_FOLDER
else
CFLAGS += --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER
endif
else
empty:=
space:= $(empty) $(empty)
CLANGVERSIONSTRING := $(shell expr `$(CXX) -dumpversion`)
#Create version number without "."
CLANGVERSION := $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f1 -d.)
CLANGVERSION += $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f2 -d.)
CLANGVERSION += $(shell expr `echo $(GCCVERSIONSTRING)` | cut -f3 -d.)
# Make sure the version number has at least 3 decimals
CLANGVERSION += 00
# Remove spaces from the version number
CLANGVERSION := $(subst $(space),$(empty),$(GCCVERSION))
# Crop the version number to 3 decimals.
CLANGVERSION := $(shell expr `echo $(GCCVERSION)` | cut -b1-3)
INT_CLANG_VERSION := $(shell expr `echo $(GCCVERSION)` \>= 360)
ifeq "$(INT_CLANG_VERSION)" "1"
CFLAGS += --std=c++11 -DMINIA_IS_IN_PARENT_FOLDER
else
CFLAGS += --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER
endif
endif
CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
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 commons.cpp IterativeExtensions.cpp Fragment_Bank.cpp Fragment.cpp GraphOutput.cpp
OBJ= $(SRC:.cpp=.o)
all: $(EXEC)
ifeq ($(prof),1)
CFLAGS+= -pg
endif
ifeq ($(unitig),1)
CFLAGS+= -DUNITIG
endif
ifeq ($(deb),1)
CFLAGS+= -O0 -DASSERTS -g
endif
ifeq ($(omp),1)
CFLAGS=-O4 -fopenmp -DOMP=1
endif
k := 0$(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_extend: $(OBJ) $(OBJ2) mapsembler_extend.cpp
#mapsembler: $(OBJ) $(OBJ2) test.cpp
$(CXX) -o $@ $^ $(CFLAGS) $(LDFLAGS)
%.o: %.cpp %.h
$(CXX) -o $@ -c $< $(CFLAGS)
#%.o: %.c %.h
# $(CC) -o $@ -c $< $(CFLAGS)
clean:
rm -rf *.o ../minia/*.o read_coherence_mapsembler/*.o
|
