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GCLDIR := $(if $(GCLDIR),$(GCLDIR),../gclib)
SEARCHDIRS := -I. -I${GCLDIR}
SYSTYPE := $(shell uname)
CXX := $(if $(CXX),$(CXX),g++)
LINKER := $(if $(LINKER),$(LINKER),g++)
LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
BASEFLAGS := -Wall -Wextra -std=c++11 ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing \
-fno-exceptions -fno-rtti
GCCV8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8)
ifeq "$(GCCV8)" "1"
BASEFLAGS += -Wno-class-memaccess
endif
CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS))
ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
# -- release build
LIBS :=
ifneq (,$(findstring static,$(MAKECMDGOALS)))
LDFLAGS += -static-libstdc++ -static-libgcc
endif
CXXFLAGS := -O3 -DNDEBUG $(CXXFLAGS)
else #debug builds
ifneq (,$(filter %profile %gprof %prof, $(MAKECMDGOALS)))
CXXFLAGS += -pg -O0 -DNDEBUG
LDFLAGS += -pg
else
#CXXFLAGS += -g -O0 -DNDEBUG
CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
endif
ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
#use sanitizer in gcc 4.9+
MEMCHECK_BUILD := 1
GCCVER49 := $(shell expr `${CXX} -dumpversion | cut -f1,2 -d.` \>= 4.9)
ifeq "$(GCCVER49)" "0"
$(error gcc version 4.9 or greater is required for this build target)
endif
CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
GCCVER5 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 5)
ifeq "$(GCCVER5)" "1"
CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
#CXXFLAGS += -fcheck-pointer-bounds -mmpx
endif
CXXFLAGS += -fno-common -fstack-protector
LIBS := -lasan -lubsan -ldl $(LIBS)
else
#just plain debug build
DEBUG_BUILD := 1
endif
endif
#ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS)))
# CXXFLAGS += -DGMEMTRACE
# OBJS += ${GDIR}/proc_mem.o
#endif
#ifdef DEBUG_BUILD
# #$(warning Building DEBUG version of stringtie.. )
# DBG_WARN=@echo
# DBG_WARN+='WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program.'
#endif
%.o : %.cpp
${CXX} ${CPPFLAGS} ${CXXFLAGS} -c $< -o $@
# C/C++ linker
OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArgs.o ${GCLDIR}/GFaSeqGet.o \
${GCLDIR}/gdna.o ${GCLDIR}/codons.o ${GCLDIR}/gff.o ${GCLDIR}/GStr.o \
${GCLDIR}/GFastaIndex.o gff_utils.o
.PHONY : all
all static release debug memcheck memdebug profile gprof prof: gffread
../gclib:
git clone https://github.com/gpertea/gclib.git ../gclib
$(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
gff_utils.o : gff_utils.h $(GCLDIR)/gff.h
${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh
${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h
gffread: gffread.o gff_utils.o
${LINKER} ${CPPFLAGS} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} -lgclib ${LIBS} -pthread
# @echo
# ${DBG_WARN}
# target for removing all object files
.PHONY : clean
clean:
@${RM} gffread gffread.o* gffread.exe $(OBJS)
@${RM} core.*
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