83 lines
2.8 KiB
Makefile
83 lines
2.8 KiB
Makefile
CFLAGS= -g -Wall -O2 -Wc++-compat
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CPPFLAGS= -DHAVE_KALLOC
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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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PROG= minimap2
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PROG_EXTRA= sdust minimap2-lite
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LIBS= -lm -lz -lpthread
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ifeq ($(sse2only),)
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
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else
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OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
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endif
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.SUFFIXES:.c .o
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.c.o:
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$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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extra:all $(PROG_EXTRA)
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minimap2:main.o getopt.o libminimap2.a
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$(CC) $(CFLAGS) main.o getopt.o -o $@ -L. -lminimap2 $(LIBS)
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minimap2-lite:example.o libminimap2.a
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$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
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libminimap2.a:$(OBJS)
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$(AR) -csru $@ $(OBJS)
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sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
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$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
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ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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clean:
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rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg*
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depend:
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(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
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# DO NOT DELETE
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align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
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bseq.o: bseq.h kseq.h
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chain.o: minimap.h mmpriv.h bseq.h kalloc.h
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example.o: minimap.h kseq.h
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format.o: kalloc.h mmpriv.h minimap.h bseq.h
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getopt.o: getopt.h
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hit.o: mmpriv.h minimap.h bseq.h kalloc.h
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index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
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kalloc.o: kalloc.h
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ksw2_extd2_sse.o: ksw2.h kalloc.h
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ksw2_exts2_sse.o: ksw2.h kalloc.h
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ksw2_extz2_sse.o: ksw2.h kalloc.h
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ksw2_ll_sse.o: ksw2.h kalloc.h
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main.o: bseq.h minimap.h mmpriv.h getopt.h
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map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
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misc.o: minimap.h ksort.h
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sdust.o: kalloc.h kdq.h kvec.h sdust.h
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sketch.o: kvec.h kalloc.h minimap.h
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