From 9e6fdd376b5e6abb4ca7f4540f79eec7b8271a78 Mon Sep 17 00:00:00 2001
From: mbrcic <mario.brcic@fer.hr>
Date: Mon, 20 Apr 2020 18:28:06 +0200
Subject: [PATCH] Changed sse2neon with SIMDe. Added building non-SIMD version.

---
 .gitmodules      |  3 +++
 Makefile         | 31 ++++++++++++++++++++++++-------
 ksw2_extd2_sse.c |  6 ++++--
 ksw2_exts2_sse.c |  7 ++++---
 ksw2_extz2_sse.c |  6 ++++--
 ksw2_ll_sse.c    |  3 ++-
 lib/simde        |  1 +
 7 files changed, 42 insertions(+), 15 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 lib/simde

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..a80f848
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "lib/simde"]
+	path = lib/simde
+	url = https://github.com/nemequ/simde.git
diff --git a/Makefile b/Makefile
index 18622f5..61c4097 100644
--- a/Makefile
+++ b/Makefile
@@ -1,11 +1,13 @@
 CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 CPPFLAGS=	-DHAVE_KALLOC
-INCLUDES=
-OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
+INCLUDES=   -Ilib/simde/simde
+OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o 
 PROG=		minimap2
 PROG_EXTRA=	sdust minimap2-lite
 LIBS=		-lm -lz -lpthread
 
+ifeq ($(no_simd),) # if no_simd is not defined
+	OBJS+=ksw2_ll_sse.o
 ifeq ($(arm_neon),) # if arm_neon is not defined
 ifeq ($(sse2only),) # if sse2only is not defined
 	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
@@ -14,13 +16,15 @@ else                # if sse2only is defined
 endif
 else				# if arm_neon is defined
 	OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
-    INCLUDES+=-Isse2neon
 ifeq ($(aarch64),)	#if aarch64 is not defined
 	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
 else				#if aarch64 is defined
 	CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
 endif
 endif
+else
+	OBJS+=ksw2_ll_nosimd.o ksw2_extz2_nosimd.o ksw2_extd2_nosimd.o ksw2_exts2_nosimd.o
+endif
 
 ifneq ($(asan),)
 	CFLAGS+=-fsanitize=address
@@ -83,15 +87,28 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
 		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 # NEON-specific targets on ARM
-
 ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
 
 ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
 
 ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
+
+# no-SIMD version
+
+ksw2_ll_nosimd.o:ksw2_ll_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
+
+ksw2_extz2_nosimd.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
+
+ksw2_extd2_nosimd.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
+
+ksw2_exts2_nosimd.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES  -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
 
 # other non-file targets
 
diff --git a/ksw2_extd2_sse.c b/ksw2_extd2_sse.c
index b578274..10c42fd 100644
--- a/ksw2_extd2_sse.c
+++ b/ksw2_extd2_sse.c
@@ -4,14 +4,16 @@
 #include "ksw2.h"
 
 #ifdef __SSE2__
-#include <emmintrin.h>
+//#include <emmintrin.h>
+#include <x86/sse2.h>
 
 #ifdef KSW_SSE2_ONLY
 #undef __SSE4_1__
 #endif
 
 #ifdef __SSE4_1__
-#include <smmintrin.h>
+//#include <smmintrin.h>
+#include <x86/sse4.1.h>
 #endif
 
 #ifdef KSW_CPU_DISPATCH
diff --git a/ksw2_exts2_sse.c b/ksw2_exts2_sse.c
index e7984c6..93efeb4 100644
--- a/ksw2_exts2_sse.c
+++ b/ksw2_exts2_sse.c
@@ -4,14 +4,15 @@
 #include "ksw2.h"
 
 #ifdef __SSE2__
-#include <emmintrin.h>
-
+//#include <emmintrin.h>
+#include <x86/sse2.h>
 #ifdef KSW_SSE2_ONLY
 #undef __SSE4_1__
 #endif
 
 #ifdef __SSE4_1__
-#include <smmintrin.h>
+//#include <smmintrin.h>
+#include <x86/sse4.1.h>
 #endif
 
 #ifdef KSW_CPU_DISPATCH
diff --git a/ksw2_extz2_sse.c b/ksw2_extz2_sse.c
index 02bb4c2..c13fcb9 100644
--- a/ksw2_extz2_sse.c
+++ b/ksw2_extz2_sse.c
@@ -3,14 +3,16 @@
 #include "ksw2.h"
 
 #ifdef __SSE2__
-#include <emmintrin.h>
+//#include <emmintrin.h>
+#include <x86/sse2.h>
 
 #ifdef KSW_SSE2_ONLY
 #undef __SSE4_1__
 #endif
 
 #ifdef __SSE4_1__
-#include <smmintrin.h>
+//#include <smmintrin.h>
+#include <x86/sse4.1.h>
 #endif
 
 #ifdef KSW_CPU_DISPATCH
diff --git a/ksw2_ll_sse.c b/ksw2_ll_sse.c
index 469de52..0359f00 100644
--- a/ksw2_ll_sse.c
+++ b/ksw2_ll_sse.c
@@ -1,7 +1,8 @@
 #include <stdlib.h>
 #include <stdint.h>
 #include <string.h>
-#include <emmintrin.h>
+//#include <emmintrin.h>
+#include <x86/sse2.h>
 #include "ksw2.h"
 
 #ifdef __GNUC__
diff --git a/lib/simde b/lib/simde
new file mode 160000
index 0000000..b30129b
--- /dev/null
+++ b/lib/simde
@@ -0,0 +1 @@
+Subproject commit b30129b3b48a6823013da2b309c50a081177b6b8