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#-- for now these MUST point to the included samtools-0.x.x and gclib subdirectories
BAM := ./samtools-0.1.18
GDIR := ./gclib
#--
INCDIRS := -I. -I${GDIR} -I${BAM}
#CXX ?= g++
CXX := $(if $(CXX),$(CXX),g++)
BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
#for gcc 8+ add: -Wno-class-memaccess
LINKER := $(if $(LINKER),$(LINKER),g++)
LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
LDFLAGS += -L${BAM}
LIBS := -lbam -lz
ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
NOTHREADS=1
endif
#detect MinGW (Windows environment)
ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
WINDOWS=1
endif
# MinGW32 GCC 4.5 link problem fix
#ifdef WINDOWS
ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
STATIC_CLIB=1
endif
#endif
# Misc. system commands
ifdef WINDOWS
RM = del /Q
else
RM = rm -f
endif
# File endings
ifdef WINDOWS
EXE = .exe
else
EXE =
endif
# Non-windows systems need pthread
ifndef WINDOWS
ifndef NOTHREADS
LIBS += -lpthread
endif
endif
ifdef NOTHREADS
BASEFLAGS += -DNOTHREADS
endif
DMACH := $(shell g++ -dumpmachine)
ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
# -- release build
RELEASE_BUILD=1
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
CXXFLAGS += -DNDEBUG $(BASEFLAGS)
else
ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
#use sanitizer in gcc 4.9+
MEMCHECK_BUILD=1
GCCVER49 := $(shell expr `g++ -dumpversion | cut -f1,2 -d.` \>= 4.9)
ifeq "$(GCCVER49)" "0"
$(error gcc version 4.9 or greater is required for this build target)
endif
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
ifeq "$(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 += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
LIBS := -lasan -lubsan -ldl $(LIBS)
else
#just plain debug build
DEBUG_BUILD=1
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
ifneq (, $(findstring darwin, $(DMACH)))
CXXFLAGS += -gdwarf-3
endif
CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
endif
endif
ifdef RELEASE_BUILD
ifneq (,$(findstring static, $(MAKECMDGOALS)))
STATIC_CLIB=1
endif
endif
ifdef STATIC_CLIB
LDFLAGS += -static-libstdc++ -static-libgcc
endif
ifdef DEBUG_BUILD
#$(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
OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o
ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS)))
CXXFLAGS += -DGMEMTRACE
OBJS += ${GDIR}/proc_mem.o
endif
ifndef NOTHREADS
OBJS += ${GDIR}/GThreads.o
endif
%.o : %.cpp
${CXX} ${CXXFLAGS} -c $< -o $@
OBJS += rlink.o tablemaker.o tmerge.o
all release static debug: stringtie${EXE}
memcheck memdebug: stringtie${EXE}
memuse memusage memtrace: stringtie${EXE}
nothreads: stringtie${EXE}
${GDIR}/GBam.o : $(GDIR)/GBam.h
stringtie.o : $(GDIR)/GBitVec.h $(GDIR)/GHash.hh $(GDIR)/GBam.h
rlink.o : rlink.h tablemaker.h $(GDIR)/GBam.h $(GDIR)/GBitVec.h
tmerge.o : rlink.h tmerge.h
tablemaker.o : tablemaker.h rlink.h
${BAM}/libbam.a:
cd ${BAM} && make lib
stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
@echo
${DBG_WARN}
.PHONY : clean cleanall cleanAll allclean
# target for removing all object files
# echo $(PATH)
clean:
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*
allclean cleanAll cleanall:
cd ${BAM} && make clean
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*