--- /dev/null
+#include <stdlib.h>
+#include <stdint.h>
+#include <emmintrin.h>
+#include "ksw.h"
+
+#include <stdio.h>
+
+struct _ksw_query_t {
+ int slen;
+ uint8_t shift;
+ uint8_t *mem;
+ __m128i *qp, *H0, *H1, *E;
+};
+
+ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat)
+{
+ ksw_query_t *q;
+ uint8_t *aligned;
+ int8_t *t;
+ int qlenp, slen, a, tmp;
+
+ q = calloc(1, sizeof(ksw_query_t));
+ q->slen = slen = (qlen + p - 1) / p; // length of segment
+ qlenp = slen * p; // qlenp can be divided by p
+ q->mem = malloc(64 + qlenp * (m + 2));
+ aligned = (uint8_t*)(((size_t)q->mem + 15) & ~0xful); // align memory
+ q->qp = (__m128i*)aligned;
+ q->H0 = q->qp + qlenp * m;
+ q->H1 = q->H0 + qlenp;
+ q->E = q->H1 + qlenp;
+ // compute shift
+ tmp = m * m;
+ for (a = 0, q->shift = 127; a < tmp; ++a) // find the minimum score (should be negative)
+ if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
+ q->shift = 256 - q->shift;
+ // An example: p=8, qlen=19, slen=3 and segmentation:
+ // {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
+ t = (int8_t*)q->qp;
+ for (a = 0; a < m; ++a) {
+ int i, k;
+ const int8_t *ma = mat + a * m;
+ for (i = 0; i < slen; ++i)
+ for (k = i; k < qlenp; k += slen) { // p iterations
+ *t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
+ //printf("%d,%d,%d,%d\n", a, i, k, *(t-1));
+ }
+ }
+ return q;
+}
+
+void ksw_qdestroy(ksw_query_t *q)
+{
+ if (!q) return;
+ free(q->mem); free(q);
+}
+
+int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, unsigned _e) // the first gap costs -(_o+_e)
+{
+ int slen, i, score;
+ __m128i zero, gapo, gape, shift, gmax, *H0, *H1, *E;
+
+#define __set_16(ret, xx) do { \
+ uint16_t t16 = ((uint16_t)(xx) << 8) | ((uint16_t)(xx) & 0x00ff); \
+ (ret) = _mm_insert_epi16((ret), t16, 0); \
+ (ret) = _mm_shufflelo_epi16((ret), 0); \
+ (ret) = _mm_shuffle_epi32((ret), 0); \
+ } while (0)
+
+#define __max_16(ret, xx) do { \
+ __m128i t; \
+ t = _mm_srli_si128((xx), 8); \
+ (xx) = _mm_max_epu8((xx), t); \
+ t = _mm_srli_si128((xx), 4); \
+ (xx) = _mm_max_epu8((xx), t); \
+ t = _mm_srli_si128((xx), 2); \
+ (xx) = _mm_max_epu8((xx), t); \
+ t = _mm_srli_si128((xx), 1); \
+ (xx) = _mm_max_epu8((xx), t); \
+ (ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \
+ } while (0)
+
+ // initialization
+ zero = _mm_xor_si128(zero, zero);
+ gmax = _mm_xor_si128(gmax, gmax);
+ __set_16(gapo, _o + _e);
+ __set_16(gape, _e);
+ H0 = q->H0; H1 = q->H1; E = q->E;
+ slen = q->slen;
+ __set_16(shift, q->shift);
+ for (i = 0; i < slen; ++i) {
+ _mm_store_si128(E + i, zero);
+ _mm_store_si128(H0 + i, zero);
+ }
+ // the core loop
+ for (i = 0; i < tlen; ++i) {
+ int j, cmp;
+ __m128i e, h, f, max, t, *S = q->qp + target[i] * slen; // s is the 1st score vector
+ max = _mm_xor_si128(max, max);
+ f = _mm_xor_si128(f, f);
+ h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
+ h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x86 is little-endian
+ for (score=0;score<16;++score)printf("%d ", ((int8_t*)&S[0])[score]);printf("\n");
+ for (j = 0; j < slen; ++j) {
+ // at the beginning, h=H'(i-1,j-1)
+ h = _mm_adds_epu8(h, S[j]); h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
+ e = _mm_load_si128(E + j); // e=E'(i,j)
+ h = _mm_max_epu8(h, e);
+ h = _mm_max_epu8(h, f); // h=H'(i,j)
+ max = _mm_max_epu8(max, h); // set max
+ for (score=0;score<16;++score)printf("%d ", ((int8_t*)&h)[score]);printf("\n");
+ _mm_store_si128(H1 + j, h); // save to H'(i,j)
+ // now compute E(i+1,j)
+ h = _mm_subs_epu8(h, gapo); // h=H'(i,j)-gapo
+ e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape
+ e = _mm_max_epu8(e, h); // e=E'(i+1,j)
+ _mm_store_si128(E + j, e); // save to E'(i+1,j)
+ // now compute F'(i,j+1)
+ f = _mm_subs_epu8(f, gape);
+ f = _mm_max_epu8(f, h);
+ // get H'(i-1,j) and prepare for the next j
+ h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
+ }
+ gmax = _mm_max_epu8(gmax, max);
+ j = 0;
+ h = _mm_load_si128(H1); // h=H(i,0); h->{0,3,6,9,12,15,18,-1}
+ f = _mm_slli_si128(f, 1); // f->{-1,3,6,9,12,15,18,-1}
+ t = _mm_subs_epu8(h, gapo); t = _mm_subs_epu8(f, t);
+ t = _mm_cmpeq_epi8(t, zero); cmp = _mm_movemask_epi8(t); // test whether s>0
+ while (cmp != 0xffff) { // the lazy-F loop
+ h = _mm_max_epu8(h, f);
+ _mm_store_si128(H1 + j, h);
+ e = _mm_load_si128(E + j); // e=E'(i,j)
+ h = _mm_subs_epu8(h, gapo); // h=H(i,j)-gapo
+ e = _mm_max_epu8(e, h); // e=E(i,j)
+ _mm_store_si128(E + j, e); // save to E(i,j)
+ f = _mm_subs_epu8(f, gape); // f-=gape
+ if (++j >= slen) j = 0, f = _mm_slli_si128(f, 1); // restart
+ h = _mm_load_si128(H1 + j);
+ t = _mm_subs_epu8(h, gapo); t = _mm_subs_epu8(f, t);
+ t = _mm_cmpeq_epi8(t, zero); cmp = _mm_movemask_epi8(t);
+ }
+ S = H1; H1 = H0; H0 = S; // swap H0 and H1
+ }
+ __max_16(score, gmax);
+ return score;
+}
+
+int main()
+{
+ int8_t mat[] = {1, -3, -3, 1};
+ uint8_t *t = (uint8_t*)"\1\0\1\1\0\0";
+ uint8_t *q = (uint8_t*)"\1\1";
+ ksw_query_t *qq = ksw_qinit(2, q, 16, 2, mat);
+ int s = ksw_sse2_16(qq, 6, t, 5, 2);
+ ksw_qdestroy(qq);
+ printf("%d\n", s);
+ return 0;
+}
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