Package: minimap2 / 2.24+dfsg-3

simde Patch series | download
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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