2017-07-19 01:56:51 +08:00
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CFLAGS= -g -Wall -O2 -Wc++-compat
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2017-06-27 03:41:55 +08:00
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CPPFLAGS= -DHAVE_KALLOC
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2017-09-04 02:29:49 +08:00
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INCLUDES=
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o ksw2_ll_sse.o
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2017-04-08 03:30:30 +08:00
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PROG= minimap2
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2017-07-19 02:48:46 +08:00
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PROG_EXTRA= sdust minimap2-lite
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2017-04-08 03:30:30 +08:00
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LIBS= -lm -lz -lpthread
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2017-09-04 08:29:24 +08:00
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ifeq ($(sse2only),)
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2017-09-04 02:29:49 +08:00
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
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else
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OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
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endif
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2017-07-19 01:56:51 +08:00
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2017-04-08 03:30:30 +08:00
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.SUFFIXES:.c .o
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.c.o:
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$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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extra:all $(PROG_EXTRA)
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2017-09-01 20:20:34 +08:00
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minimap2:main.o getopt.o libminimap2.a
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$(CC) $(CFLAGS) main.o getopt.o -o $@ -L. -lminimap2 $(LIBS)
|
2017-04-08 03:30:30 +08:00
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|
2017-07-19 02:43:43 +08:00
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minimap2-lite:example.o libminimap2.a
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|
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$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
|
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|
|
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|
2017-04-08 03:30:30 +08:00
|
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|
libminimap2.a:$(OBJS)
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|
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$(AR) -csru $@ $(OBJS)
|
|
|
|
|
|
2017-09-03 05:52:33 +08:00
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|
sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
|
|
|
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|
$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
|
2017-04-08 03:30:30 +08:00
|
|
|
|
2017-09-04 02:29:49 +08:00
|
|
|
ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
|
2017-09-04 08:29:24 +08:00
|
|
|
$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
|
2017-09-04 02:29:49 +08:00
|
|
|
|
|
|
|
|
ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
|
2017-09-04 08:29:24 +08:00
|
|
|
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
|
2017-09-04 02:29:49 +08:00
|
|
|
|
|
|
|
|
ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
|
2017-09-04 08:29:24 +08:00
|
|
|
$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
|
2017-09-04 02:29:49 +08:00
|
|
|
|
|
|
|
|
ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
|
2017-09-04 08:29:24 +08:00
|
|
|
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
|
2017-09-04 02:29:49 +08:00
|
|
|
|
|
|
|
|
ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
|
2017-09-04 08:29:24 +08:00
|
|
|
$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
|
2017-09-04 02:29:49 +08:00
|
|
|
|
|
|
|
|
ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
|
2017-09-04 08:29:24 +08:00
|
|
|
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
|
2017-09-04 02:29:49 +08:00
|
|
|
|
|
|
|
|
ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
|
|
|
|
|
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
|
|
|
|
|
|
2017-04-08 03:30:30 +08:00
|
|
|
clean:
|
2017-09-17 12:05:30 +08:00
|
|
|
rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg*
|
2017-04-08 03:30:30 +08:00
|
|
|
|
|
|
|
|
depend:
|
2017-07-08 22:26:00 +08:00
|
|
|
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
|
2017-04-08 03:30:30 +08:00
|
|
|
|
|
|
|
|
# DO NOT DELETE
|
|
|
|
|
|
2017-07-08 22:26:00 +08:00
|
|
|
align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
|
2017-04-08 03:30:30 +08:00
|
|
|
bseq.o: bseq.h kseq.h
|
2017-06-26 04:13:54 +08:00
|
|
|
chain.o: minimap.h mmpriv.h bseq.h kalloc.h
|
2017-07-19 02:48:46 +08:00
|
|
|
example.o: minimap.h kseq.h
|
2017-08-11 03:04:59 +08:00
|
|
|
format.o: kalloc.h mmpriv.h minimap.h bseq.h
|
2017-09-03 05:52:33 +08:00
|
|
|
getopt.o: getopt.h
|
2017-06-30 07:35:38 +08:00
|
|
|
hit.o: mmpriv.h minimap.h bseq.h kalloc.h
|
2017-06-06 22:16:33 +08:00
|
|
|
index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
|
2017-04-08 03:30:30 +08:00
|
|
|
kalloc.o: kalloc.h
|
2017-07-08 22:26:00 +08:00
|
|
|
ksw2_extd2_sse.o: ksw2.h kalloc.h
|
2017-08-13 06:54:32 +08:00
|
|
|
ksw2_exts2_sse.o: ksw2.h kalloc.h
|
2017-07-08 22:26:00 +08:00
|
|
|
ksw2_extz2_sse.o: ksw2.h kalloc.h
|
2017-07-30 11:52:30 +08:00
|
|
|
ksw2_ll_sse.o: ksw2.h kalloc.h
|
2017-09-03 05:52:33 +08:00
|
|
|
main.o: bseq.h minimap.h mmpriv.h getopt.h
|
2017-06-26 04:13:54 +08:00
|
|
|
map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
|
2017-04-08 03:30:30 +08:00
|
|
|
misc.o: minimap.h ksort.h
|
|
|
|
|
sdust.o: kalloc.h kdq.h kvec.h sdust.h
|
|
|
|
|
sketch.o: kvec.h kalloc.h minimap.h
|
