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CXX ?= g++
CC ?= gcc
CXXFLAGS ?= -O2
LFLAGS = -lz
all: nxtrim
debug: CXXFLAGS += -Wall -g
debug: all
GIT_HASH := $(shell git describe --abbrev=4 --always )
VERSION = v0.4.3
GIT_VERSION =
ifneq "$(wildcard .git)" ""
GIT_VERSION = -$(shell git describe --always)
endif
version.h:
echo '#define VERSION "$(VERSION)$(GIT_VERSION)"' > $@
OBJS=matepair.o fastqlib.o utilityfunc.o
.cpp.o:
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<
nxtrim: nxtrim.cpp $(OBJS) version.h
$(CXX) $(CPPFLAGS) $(CXXFLAGS) nxtrim.cpp $(OBJS) $(LFLAGS) -o $@ $(LDFLAGS)
matepair.o: matepair.cpp matepair.h fastqlib.h
fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h
utilityfunc.o: utilityfunc.cpp utilityfunc.h
test: nxtrim
bash -e example/run_test.sh
ecmg: nxtrim
cd test/;bash -e ecmg.sh
clean:
rm -f $(OBJS) nxtrim version.h
rm -rf test/output_dir/
rm -f test/*bam test/*pe.fastq.gz test/*mp.fastq.gz test/*unknown.fastq.gz
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