On other platforms, emulate SSE2 SIMD calls using scalar code

Makefile

@@ -78,7 +78,7 @@ fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
 is.o: malloc_wrap.h
 kopen.o: malloc_wrap.h
 kstring.o: kstring.h malloc_wrap.h
-ksw.o: ksw.h neon_sse.h malloc_wrap.h
+ksw.o: ksw.h neon_sse.h scalar_sse.h malloc_wrap.h
 main.o: kstring.h malloc_wrap.h utils.h
 malloc_wrap.o: malloc_wrap.h
 maxk.o: bwa.h bntseq.h bwt.h bwamem.h kseq.h malloc_wrap.h

ksw.c

@@ -30,6 +30,8 @@
 #include <emmintrin.h>
 #elif defined __ARM_NEON
 #include "neon_sse.h"
+#else
+#include "scalar_sse.h"
 #endif
 #include "ksw.h"
 
@@ -139,6 +141,10 @@ kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del
 #elif defined __ARM_NEON
 #define __max_16(ret, xx) (ret) = vmaxvq_u8((xx))
 #define allzero_16(xx) (vmaxvq_u8((xx)) == 0)
+
+#else
+#define __max_16(ret, xx) (ret) = m128i_max_u8((xx))
+#define allzero_16(xx) (m128i_allzero((xx)))
 #endif
 
 	// initialization
@@ -267,6 +273,10 @@ kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_de
 #elif defined __ARM_NEON
 #define __max_8(ret, xx) (ret) = vmaxvq_s16(vreinterpretq_s16_u8((xx)))
 #define allzero_0f_8(xx) (vmaxvq_u16(vreinterpretq_u16_u8((xx))) == 0)
+
+#else
+#define __max_8(ret, xx) (ret) = m128i_max_s16((xx))
+#define allzero_0f_8(xx) (m128i_allzero((xx)))
 #endif
 
 	// initialization

scalar_sse.h

@@ -0,0 +1,119 @@
+#ifndef SCALAR_SSE_H
+#define SCALAR_SSE_H
+
+#include <assert.h>
+#include <stdint.h>
+#include <string.h>
+
+typedef union m128i {
+	uint8_t u8[16];
+	int16_t i16[8];
+} __m128i;
+
+static inline __m128i _mm_set1_epi32(int32_t n) {
+	assert(n >= 0 && n <= 255);
+	__m128i r; memset(&r, n, sizeof r); return r;
+}
+
+static inline __m128i _mm_load_si128(const __m128i *ptr) { __m128i r; memcpy(&r, ptr, sizeof r); return r; }
+static inline void _mm_store_si128(__m128i *ptr, __m128i a) { memcpy(ptr, &a, sizeof a); }
+
+static inline int m128i_allzero(__m128i a) {
+	static const char zero[] = "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
+	return memcmp(&a, zero, sizeof a) == 0;
+}
+
+static inline __m128i _mm_slli_si128(__m128i a, int n) {
+	int i;
+	memmove(&a.u8[n], &a.u8[0], 16 - n);
+	for (i = 0; i < n; i++) a.u8[i] = 0;
+	return a;
+}
+
+static inline __m128i _mm_adds_epu8(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 16; i++) {
+		uint16_t aa = a.u8[i];
+		aa += b.u8[i];
+		a.u8[i] = (aa < 256)? aa : 255;
+	}
+	return a;
+}
+
+static inline __m128i _mm_max_epu8(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 16; i++)
+		if (a.u8[i] < b.u8[i]) a.u8[i] = b.u8[i];
+	return a;
+}
+
+static inline uint8_t m128i_max_u8(__m128i a) {
+	uint8_t max = 0;
+	int i;
+	for (i = 0; i < 16; i++)
+		if (max < a.u8[i]) max = a.u8[i];
+	return max;
+}
+
+static inline __m128i _mm_set1_epi8(int8_t n) { __m128i r; memset(&r, n, sizeof r); return r; }
+
+static inline __m128i _mm_subs_epu8(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 16; i++) {
+		int16_t aa = a.u8[i];
+		aa -= b.u8[i];
+		a.u8[i] = (aa >= 0)? aa : 0;
+	}
+	return a;
+}
+
+static inline __m128i _mm_adds_epi16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++) {
+		int32_t aa = a.i16[i];
+		aa += b.i16[i];
+		a.i16[i] = (aa < 32768)? aa : 32767;
+	}
+	return a;
+}
+
+static inline __m128i _mm_cmpgt_epi16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++)
+		a.i16[i] = (a.i16[i] > b.i16[i])? 0xffff : 0x0000;
+	return a;
+}
+
+static inline __m128i _mm_max_epi16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++)
+		if (a.i16[i] < b.i16[i]) a.i16[i] = b.i16[i];
+	return a;
+}
+
+static inline __m128i _mm_set1_epi16(int16_t n) {
+	__m128i r;
+	r.i16[0] = r.i16[1] = r.i16[2] = r.i16[3] =
+	r.i16[4] = r.i16[5] = r.i16[6] = r.i16[7] = n;
+	return r;
+}
+
+static inline int16_t m128i_max_s16(__m128i a) {
+	int16_t max = -32768;
+	int i;
+	for (i = 0; i < 8; i++)
+		if (max < a.i16[i]) max = a.i16[i];
+	return max;
+}
+
+static inline __m128i _mm_subs_epu16(__m128i a, __m128i b) {
+	int i;
+	for (i = 0; i < 8; i++) {
+		int32_t aa = a.i16[i];
+		aa -= b.i16[i];
+		a.i16[i] = (aa >= 0)? aa : 0;
+	}
+	return a;
+}
+
+#endif