3 CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
5 DFLAGS= -D_FILE_OFFSET_BITS=64
7 PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
14 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
18 lib-recur all-recur clean-recur cleanlocal-recur install-recur:
19 @target=`echo $@ | sed s/-recur//`; \
21 list='$(SUBDIRS)'; for subdir in $$list; do \
23 $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
24 INCLUDES="$(INCLUDES)" $$target || exit 1; \
31 $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
33 bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
34 $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
37 $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
40 $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
42 md5fa:md5.o md5fa.o md5.h ../kseq.h
43 $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
45 md5sum-lite:md5sum-lite.o
46 $(CC) $(CFLAGS) -o $@ md5sum-lite.o
48 md5sum-lite.o:md5.c md5.h
49 $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
51 maq2sam-short:maq2sam.c
52 $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
54 maq2sam-long:maq2sam.c
55 $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
58 $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
60 wgsim.o:wgsim.c ../kseq.h
61 $(CC) $(CFLAGS) -c -I.. -o $@ wgsim.c
63 ace2sam.o:ace2sam.c ../kstring.h ../kseq.h
64 $(CC) $(CFLAGS) -c -I.. -o $@ ace2sam.c
67 rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a
69 clean:cleanlocal-recur