--- Makefile.simde.orig	2021-11-18 22:11:48 UTC
+++ Makefile.simde
@@ -1,13 +1,26 @@
-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
+
+# Makefile patches rejected by upstream
+
+CFLAGS?=	-g -Wall -O2
+CFLAGS+=	-Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__
+CPPFLAGS?=	-DHAVE_KALLOC
+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
 PROG=		minimap2
 PROG_EXTRA=	sdust minimap2-lite
 LIBS=		-lm -lz -lpthread
 
+PREFIX?=	/usr/local
+MAN1DIR?=	${PREFIX}/man/man1
+DATADIR?=	${PREFIX}/share/minimap2
 
+MKDIR?=		mkdir
+CP?=		cp	
+INSTALL?=	install
+STRIP?=		strip
+
 ifneq ($(arm_neon),) # if arm_neon is defined
 ifeq ($(aarch64),)   #if aarch64 is not defined
 	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
@@ -26,7 +39,7 @@ ifneq ($(tsan),)
 	LIBS+=-fsanitize=thread
 endif
 
-.PHONY:all extra clean depend
+.PHONY:all extra install install-strip clean depend
 .SUFFIXES:.c .o
 
 .c.o:
@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
 		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
 
 # other non-file targets
+
+
+install: all
+	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+	${MKDIR} -p ${DESTDIR}${MAN1DIR}
+	${MKDIR} -p ${DESTDIR}${DATADIR}
+	${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
+	${CP} -R test ${DESTDIR}${DATADIR}
+
+install-strip: install
+	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
+	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
+	${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
 
 clean:
 		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*