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--- minimap2.orig/Makefile.simde
+++ minimap2/Makefile.simde
@@ -1,8 +1,8 @@
-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
-CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
-INCLUDES= -Ilib/simde
-OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \
- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
+CFLAGS+= -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
+INCLUDES=
+OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
+ lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
+ ksw2_ll_sse.o ksw2_extz2.o ksw2_extd2.o ksw2_exts2.o
PROG= minimap2
PROG_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread
@@ -37,28 +37,27 @@
extra:all $(PROG_EXTRA)
minimap2:main.o libminimap2.a
- $(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
+ $(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)
minimap2-lite:example.o libminimap2.a
- $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+ $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)
libminimap2.a:$(OBJS)
- $(AR) -csru $@ $(OBJS)
+ rm -f $@
+ $(AR) csrD $@ $(OBJS)
-sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
- $(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+ksw2_extz2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
-ksw2_ll_simde.o:ksw2_ll_sse.c ksw2.h kalloc.h
- $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
+ksw2_extd2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
-ksw2_extz2_simde.o:ksw2_extz2_sse.c ksw2.h kalloc.h
- $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+ksw2_exts2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
-ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2.h kalloc.h
- $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
+ $(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz $(LDFLAGS)
-ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
- $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
# other non-file targets
@@ -80,9 +79,6 @@
index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h
index.o: ksort.h
kalloc.o: kalloc.h
-ksw2_extd2_sse.o: ksw2.h kalloc.h
-ksw2_exts2_sse.o: ksw2.h kalloc.h
-ksw2_extz2_sse.o: ksw2.h kalloc.h
ksw2_ll_sse.o: ksw2.h kalloc.h
kthread.o: kthread.h
main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
|
