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Makefile
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Makefile
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CC = g++
ifndef BOOST_ROOT
$(error BOOST_ROOT is undefined. Point BOOST_ROOT at your boost installation ie. BOOST_ROOT/lib and BOOST_ROOT/include should exist)
endif
LFLAGS = -L$(BOOST_ROOT)/lib -lz -lboost_iostreams -lboost_program_options
CFLAGS = -O3 -I$(BOOST_ROOT)/include
#CFLAGS = -g -I$(BOOST_ROOT)/include
all: mergeReads nxtrim test
test: test.cpp fastqlib.o utilityfunc.o matepair.o
$(CC) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o test $(LFLAGS)
githash.h:
git log -1 --format="#define HASH \"%h\"" > githash.h
nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o githash.h version.h
$(CC) $(CFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o nxtrim $(LFLAGS)
mergeReads: mergeReads.cpp fastqlib.o utilityfunc.o fastqlib.o githash.h version.h
$(CC) $(CFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads $(LFLAGS)
matepair.o: matepair.cpp matepair.h fastqlib.h
$(CC) $(CFLAGS) -c matepair.cpp
fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h
$(CC) $(CFLAGS) -c fastqlib.cpp
utilityfunc.o: utilityfunc.cpp utilityfunc.h
$(CC) $(CFLAGS) -c utilityfunc.cpp
clean:
rm *.o
rm nxtrim
rm test
rm mergeReads