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.PHONY=all cramtests
SRCDIR:=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-include ${CURDIR}/../defines.mk
include ${SRCDIR}/../rules.mk
CXXFLAGS ?= -O3 -g
CXXOPTS := -std=c++0x -pedantic \
-Wall -Wextra -Wno-overloaded-virtual \
-MMD -MP
override CXXFLAGS += ${CXXOPTS} ${GCXXFLAGS}
EXE = loadPulses pls2fasta samtoh5 samtom4 samFilter toAfg sawriter sdpMatcher
LD_LIBRARY_PATH:=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
vpath %.cpp ${SRCDIR}
all: ${EXE}
bam2bax: ${CURDIR}/bam2bax/bin/bam2bax
${CURDIR}/bam2bax/bin/bam2bax:
@cd ${CURDIR}/bam2bax && make all
bax2bam: ${CURDIR}/bax2bam/bin/bax2bam
${CURDIR}/bax2bam/bin/bax2bam:
@cd ${CURDIR}/bax2bam && make all
${EXE}:
${CXX} -o $@ $< ${CXXFLAGS} ${CPPFLAGS} -MF"${@:%=%.d}" ${STATIC} ${LDFLAGS} ${LDLIBS}
loadPulses: LoadPulses.o
pls2fasta: PulseToFasta.o
samtoh5: SamToCmpH5.o
samtom4: SamToM4.o
samFilter: SamFilter.o
toAfg: ToAfg.o
sawriter: SAWriter.o
sdpMatcher: SDPMatcher.o
CTESTS := \
ctest/loadPulses_fast.t ctest/pls2fasta_fast.t ctest/samFilter.t ctest/samtom4.t ctest/sdpMatcher.t \
ctest/loadPulses.t ctest/pls2fasta.t ctest/samtoh5.t ctest/sawriter.t ctest/toAfg.t
SLOW_CTESTS := ctest/loadPulses.t ctest/pls2fasta.t
cramtests: ${EXE}
cram -v --shell=/bin/bash ${CTESTS}
cramfast: ${EXE}
cram -v --shell=/bin/bash ${filter-out ${SLOW_CTESTS}, ${CTESTS}}
clean:
@rm -f ${EXE}
@rm -f *.d *.o
@cd ${CURDIR}/bam2bax && make clean && cd ${CURDIR}
@cd ${CURDIR}/bax2bam && make clean && cd ${CURDIR}
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