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#-- for now these MUST point to the included "samtools-0.x.x" and "gclib" sub-directories
GDIR := ./gclib
#--
INCDIRS := -I. -I${GDIR} -I/usr/include/samtools -I/usr/include/htslib
CXX := $(if $(CXX),$(CXX),g++)
BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti
#for gcc 8+ add: -Wno-class-memaccess
GCCGTE5 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 5)
ifeq "$(GCCGTE5)" "1"
BASEFLAGS += -Wno-implicit-fallthrough
endif
GCCVER8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8)
ifeq "$(GCCVER8)" "1"
BASEFLAGS += -Wno-class-memaccess
endif
LINKER := $(if $(LINKER),$(LINKER),g++)
LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
# LDFLAGS += -L${BAM}
LIBS := -lhts -lbz2 -lz -lm
ifneq (,$(filter %nothreads %prof %profile, $(MAKECMDGOALS)))
NOTHREADS=1
endif
#detect MinGW (Windows environment)
ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
WINDOWS=1
endif
# Misc. system commands
#ifdef WINDOWS ##<-- use MSYS
# RM = del /Q
#else
RM = rm -f
#endif
# Non-windows systems need pthread
ifndef WINDOWS
ifndef NOTHREADS
LIBS := -pthread ${LIBS}
BASEFLAGS += -pthread
endif
endif
ifdef NOTHREADS
BASEFLAGS += -DNOTHREADS
endif
# Compiling for Windows with MinGW?
#ifneq ($(findstring -mingw,$(shell $(CC) -dumpmachine 2>/dev/null)),)
#LIBS += -lregex -lws2_32
#endif
# File endings
ifdef WINDOWS
EXE = .exe
LIBS += -lregex -lws2_32
else
EXE =
endif
DMACH := $(shell ${CXX} -dumpmachine)
ifneq (,$(filter %release %static %static-cpp, $(MAKECMDGOALS)))
# -- release build
RELEASE_BUILD=1
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
CXXFLAGS += -DNDEBUG $(BASEFLAGS)
else
ifneq (,$(filter %memcheck %memdebug %tsan %tcheck %thrcheck, $(MAKECMDGOALS)))
ifneq "$(GCCGTE5)" "1"
$(error g++ version 5 or greater is required for this build target)
endif
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
SANLIBS :=
ifneq (,$(filter %tsan %tcheck %thrcheck, $(MAKECMDGOALS)))
# thread sanitizer only (incompatible with address sanitizer)
CXXFLAGS += -fno-omit-frame-pointer -fsanitize=thread -fsanitize=undefined $(BASEFLAGS)
SANLIBS := -ltsan
else
# address sanitizer
CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
SANLIBS := -lasan
endif
ifeq "$(GCCGTE5)" "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 := ${SANLIBS} -lubsan -ldl ${LIBS}
else
ifneq (,$(filter %prof %profile, $(MAKECMDGOALS)))
## profiling build
CXXFLAGS := -DNDEBUG $(BASEFLAGS) -g -pg
LDFLAGS += -g -pg
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 $(BASEFLAGS)
endif
endif
endif
ifdef RELEASE_BUILD
ifneq ($(findstring static,$(MAKECMDGOALS)),)
# static or static-cpp found
ifneq ($(findstring static-cpp,$(MAKECMDGOALS)),)
#not a full static build, only c/c++ libs
LDFLAGS := -static-libgcc -static-libstdc++ ${LDFLAGS}
else
#full static build
LDFLAGS := -static -static-libgcc -static-libstdc++ ${LDFLAGS}
endif
endif
endif
ifdef DEBUG_BUILD
#$(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}/GSam.o \
${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFastaIndex.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} ${CPPFLAGS} ${CXXFLAGS} -c $< -o $@
OBJS += bundle.o rlink.o tablemaker.o tmerge.o
all release static static-cpp debug: stringtie${EXE}
memcheck memdebug tsan tcheck thrcheck: stringtie${EXE}
memuse memusage memtrace: stringtie${EXE}
prof profile: stringtie${EXE}
nothreads: stringtie${EXE}
stringtie.o : $(GDIR)/GBitVec.h $(GDIR)/GHashMap.hh $(GDIR)/GSam.h
rlink.o : rlink.h tablemaker.h bundle.h $(GDIR)/GSam.h $(GDIR)/GBitVec.h
bundle.o : bundle.h rlink.h tablemaker.h $(GDIR)/GSam.h
tmerge.o : rlink.h tmerge.h
tablemaker.o : tablemaker.h rlink.h
##${BAM}/libbam.a:
## cd ${BAM} && make lib
stringtie${EXE}: $(OBJS) stringtie.o
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
@echo
${DBG_WARN}
test demo tests: stringtie${EXE}
@./run_tests.sh
.PHONY : clean clean-htslib
# target for removing all object files
# echo $(PATH)
clean:
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*
clean-all: clean
cd ${HTSLIB} && ./build_lib.sh clean
clean-htslib:
cd ${HTSLIB} && ./build_lib.sh clean
##allclean cleanAll cleanall:
## cd ${BAM} && make clean
## ${RM} stringtie${EXE} stringtie.o* $(OBJS)
## ${RM} core.*
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