56 lines
1.3 KiB
Makefile
56 lines
1.3 KiB
Makefile
CC= gcc
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CXX= g++
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CFLAGS= -g -Wall -O2
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CXXFLAGS= $(CFLAGS)
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DFLAGS= -DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
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OBJS= utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
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bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
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bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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bwtsw2_chain.o bamlite.o
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PROG= bwa
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INCLUDES=
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LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
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SUBDIRS= . bwt_gen
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.SUFFIXES:.c .o .cc
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.c.o:
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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.cc.o:
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$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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lib-recur all-recur clean-recur cleanlocal-recur install-recur:
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@target=`echo $@ | sed s/-recur//`; \
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wdir=`pwd`; \
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list='$(SUBDIRS)'; for subdir in $$list; do \
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cd $$subdir; \
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$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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INCLUDES="$(INCLUDES)" $$target || exit 1; \
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cd $$wdir; \
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done;
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lib:
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bwa:lib-recur $(OBJS) main.o
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$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
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bwt.o:bwt.h
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bwtio.o:bwt.h
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bwtaln.o:bwt.h bwtaln.h kseq.h
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bwt1away.o:bwt.h bwtaln.h
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bwt2fmv.o:bwt.h
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bntseq.o:bntseq.h
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bwtgap.o:bwtgap.h bwtaln.h bwt.h
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bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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bwtsw2_main.o:bwtsw2.h
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cleanlocal:
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rm -f gmon.out *.o a.out $(PROG) *~ *.a
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clean:cleanlocal-recur
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