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1b8cbbb @michaelglass initial commit, no changes made
authored
1 CC= gcc
2 CXX= g++
3 CFLAGS= -g -Wall -O2 -m64
4 CXXFLAGS= $(CFLAGS)
5 DFLAGS= -DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
6 OBJS= utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
7 bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
751a13e @michaelglass upgraded to 0.5.4
authored
8 bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
9 bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
10 bwtsw2_chain.o
1b8cbbb @michaelglass initial commit, no changes made
authored
11 PROG= bwa
12 INCLUDES=
13 LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
14 SUBDIRS= . bwt_gen
15
16 .SUFFIXES:.c .o .cc
17
18 .c.o:
19 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
20 .cc.o:
21 $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
22
23 all:$(PROG)
24
25 lib-recur all-recur clean-recur cleanlocal-recur install-recur:
26 @target=`echo $@ | sed s/-recur//`; \
27 wdir=`pwd`; \
28 list='$(SUBDIRS)'; for subdir in $$list; do \
29 cd $$subdir; \
30 $(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
31 INCLUDES="$(INCLUDES)" $$target || exit 1; \
32 cd $$wdir; \
33 done;
34
35 lib:
36
37 bwa:lib-recur $(OBJS) main.o
38 $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
39
40 bwt.o:bwt.h
41 bwtio.o:bwt.h
42 bwtaln.o:bwt.h bwtaln.h kseq.h
43 bwt1away.o:bwt.h bwtaln.h
44 bwt2fmv.o:bwt.h
45 bntseq.o:bntseq.h
46 bwtgap.o:bwtgap.h bwtaln.h bwt.h
47
751a13e @michaelglass upgraded to 0.5.4
authored
48 bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
49 bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
50 bwtsw2_main.o:bwtsw2.h
51
1b8cbbb @michaelglass initial commit, no changes made
authored
52 cleanlocal:
53 rm -f gmon.out *.o a.out $(PROG) *~ *.a
54
55 clean:cleanlocal-recur
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