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all:
THISDIR:=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-include ${CURDIR}/defines.mk
include ${THISDIR}/../rules.mk
CXXOPTS := -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual
SYSINCLUDES = ${HDF5_INC} ${PBBAM_INC} ${BOOST_INC}
LIBS += ${LIBPBDATA_LIB} ${LIBPBIHDF_LIB} ${HDF5_LIB} ${PBBAM_LIB} ${ZLIB_LIB}
LDFLAGS += $(patsubst %,-L%,${LIBS})
LDLIBS += -lpbdata $(HTSLIB_LIBS)
ifeq (${nohdf},)
LDLIBS+= -lpbihdf
#LDFLAGS+= -flat_namespace # so we do not need LDLIBS+= -lhdf5 -lhdf5_cpp
endif
# We might also need some -l* for pbbam, etc.
all: static shared
static: libblasr.a
shared: libblasr${SH_LIB_EXT}
paths := . simulator format files utils tuples statistics qvs suffixarray \
datastructures/alignment datastructures/alignmentset datastructures/anchoring datastructures/tuplelists \
algorithms/alignment algorithms/alignment/sdp algorithms/anchoring algorithms/compare algorithms/sorting \
query
paths := ${paths} $(patsubst %,${THISDIR}%,${paths})
sources := $(shell find ${THISDIR} -name '*.cpp')
ifdef nohdf
sources := $(filter-out ${THISDIR}files/% ${THISDIR}utils/FileOfFileNames.cpp ${THISDIR}format/SAMHeaderPrinter.cpp, $(sources))
endif
sources := $(notdir ${sources})
objects := $(sources:.cpp=.o)
shared_objects := $(sources:.cpp=.shared.o)
dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
vpath %.cpp ${paths}
libblasr.a: $(objects)
$(AR) $(ARFLAGS) $@ $^
libblasr${SH_LIB_EXT}: $(shared_objects)
clean:
rm -f libblasr.a libblasr.so *.o *.d
-include $(dependencies)
depend: $(dependencies:.d=.depend)
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