-
Notifications
You must be signed in to change notification settings - Fork 401
/
ksw2_extz2_sse.c
313 lines (301 loc) · 13 KB
/
ksw2_extz2_sse.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
#include <string.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#ifdef USE_SIMDE
#include <simde/x86/sse2.h>
#else
#include <emmintrin.h>
#endif
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#ifdef USE_SIMDE
#include <simde/x86/sse4.1.h>
#else
#include <smmintrin.h>
#endif
#endif
#ifdef KSW_CPU_DISPATCH
#ifdef __SSE4_1__
void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
#else
void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
#endif
#else
void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
#endif // ~KSW_CPU_DISPATCH
{
#define __dp_code_block1 \
z = _mm_add_epi8(_mm_load_si128(&s[t]), qe2_); \
xt1 = _mm_load_si128(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
tmp = _mm_srli_si128(xt1, 15); /* tmp <- x[r-1][t+15] */ \
xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_); /* xt1 <- x[r-1][t-1..t+14] */ \
x1_ = tmp; \
vt1 = _mm_load_si128(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
tmp = _mm_srli_si128(vt1, 15); /* tmp <- v[r-1][t+15] */ \
vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); /* vt1 <- v[r-1][t-1..t+14] */ \
v1_ = tmp; \
a = _mm_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
ut = _mm_load_si128(&u[t]); /* ut <- u[t..t+15] */ \
b = _mm_add_epi8(_mm_load_si128(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */
#define __dp_code_block2 \
z = _mm_max_epu8(z, b); /* z = max(z, b); this works because both are non-negative */ \
z = _mm_min_epu8(z, max_sc_); \
_mm_store_si128(&u[t], _mm_sub_epi8(z, vt1)); /* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \
_mm_store_si128(&v[t], _mm_sub_epi8(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \
z = _mm_sub_epi8(z, q_); \
a = _mm_sub_epi8(a, z); \
b = _mm_sub_epi8(b, z);
int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, wl, wr, max_sc, min_sc;
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX);
int32_t *H = 0, H0 = 0, last_H0_t = 0;
uint8_t *qr, *sf, *mem, *mem2 = 0;
__m128i q_, qe2_, zero_, flag1_, flag2_, flag8_, flag16_, sc_mch_, sc_mis_, sc_N_, m1_, max_sc_;
__m128i *u, *v, *x, *y, *s, *p = 0;
ksw_reset_extz(ez);
if (m <= 0 || qlen <= 0 || tlen <= 0) return;
zero_ = _mm_set1_epi8(0);
q_ = _mm_set1_epi8(q);
qe2_ = _mm_set1_epi8((q + e) * 2);
flag1_ = _mm_set1_epi8(1);
flag2_ = _mm_set1_epi8(2);
flag8_ = _mm_set1_epi8(0x08);
flag16_ = _mm_set1_epi8(0x10);
sc_mch_ = _mm_set1_epi8(mat[0]);
sc_mis_ = _mm_set1_epi8(mat[1]);
sc_N_ = mat[m*m-1] == 0? _mm_set1_epi8(-e) : _mm_set1_epi8(mat[m*m-1]);
m1_ = _mm_set1_epi8(m - 1); // wildcard
max_sc_ = _mm_set1_epi8(mat[0] + (q + e) * 2);
if (w < 0) w = tlen > qlen? tlen : qlen;
wl = wr = w;
tlen_ = (tlen + 15) / 16;
n_col_ = qlen < tlen? qlen : tlen;
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 15) / 16 + 1;
qlen_ = (qlen + 15) / 16;
for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
max_sc = max_sc > mat[t]? max_sc : mat[t];
min_sc = min_sc < mat[t]? min_sc : mat[t];
}
if (-min_sc > 2 * (q + e)) return; // otherwise, we won't see any mismatches
mem = (uint8_t*)kcalloc(km, tlen_ * 6 + qlen_ + 1, 16);
u = (__m128i*)(((size_t)mem + 15) >> 4 << 4); // 16-byte aligned
v = u + tlen_, x = v + tlen_, y = x + tlen_, s = y + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 16;
if (!approx_max) {
H = (int32_t*)kmalloc(km, tlen_ * 16 * 4);
for (t = 0; t < tlen_ * 16; ++t) H[t] = KSW_NEG_INF;
}
if (with_cigar) {
mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 16);
p = (__m128i*)(((size_t)mem2 + 15) >> 4 << 4);
off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
off_end = off + qlen + tlen - 1;
}
for (t = 0; t < qlen; ++t) qr[t] = query[qlen - 1 - t];
memcpy(sf, target, tlen);
for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {
int st = 0, en = tlen - 1, st0, en0, st_, en_;
int8_t x1, v1;
uint8_t *qrr = qr + (qlen - 1 - r), *u8 = (uint8_t*)u, *v8 = (uint8_t*)v;
__m128i x1_, v1_;
// find the boundaries
if (st < r - qlen + 1) st = r - qlen + 1;
if (en > r) en = r;
if (st < (r-wr+1)>>1) st = (r-wr+1)>>1; // take the ceil
if (en > (r+wl)>>1) en = (r+wl)>>1; // take the floor
if (st > en) {
ez->zdropped = 1;
break;
}
st0 = st, en0 = en;
st = st / 16 * 16, en = (en + 16) / 16 * 16 - 1;
// set boundary conditions
if (st > 0) {
if (st - 1 >= last_st && st - 1 <= last_en)
x1 = ((uint8_t*)x)[st - 1], v1 = v8[st - 1]; // (r-1,s-1) calculated in the last round
else x1 = v1 = 0; // not calculated; set to zeros
} else x1 = 0, v1 = r? q : 0;
if (en >= r) ((uint8_t*)y)[r] = 0, u8[r] = r? q : 0;
// loop fission: set scores first
if (!(flag & KSW_EZ_GENERIC_SC)) {
for (t = st0; t <= en0; t += 16) {
__m128i sq, st, tmp, mask;
sq = _mm_loadu_si128((__m128i*)&sf[t]);
st = _mm_loadu_si128((__m128i*)&qrr[t]);
mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));
tmp = _mm_cmpeq_epi8(sq, st);
#ifdef __SSE4_1__
tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);
tmp = _mm_blendv_epi8(tmp, sc_N_, mask);
#else
tmp = _mm_or_si128(_mm_andnot_si128(tmp, sc_mis_), _mm_and_si128(tmp, sc_mch_));
tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp), _mm_and_si128(mask, sc_N_));
#endif
_mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);
}
} else {
for (t = st0; t <= en0; ++t)
((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
}
// core loop
x1_ = _mm_cvtsi32_si128(x1);
v1_ = _mm_cvtsi32_si128(v1);
st_ = st / 16, en_ = en / 16;
assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
for (t = st_; t <= en_; ++t) {
__m128i z, a, b, xt1, vt1, ut, tmp;
__dp_code_block1;
#ifdef __SSE4_1__
z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8()
z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
#endif
__dp_code_block2;
#ifdef __SSE4_1__
_mm_store_si128(&x[t], _mm_max_epi8(a, zero_));
_mm_store_si128(&y[t], _mm_max_epi8(b, zero_));
#else
tmp = _mm_cmpgt_epi8(a, zero_);
_mm_store_si128(&x[t], _mm_and_si128(a, tmp));
tmp = _mm_cmpgt_epi8(b, zero_);
_mm_store_si128(&y[t], _mm_and_si128(b, tmp));
#endif
}
} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
__m128i *pr = p + (size_t)r * n_col_ - st_;
off[r] = st, off_end[r] = en;
for (t = st_; t <= en_; ++t) {
__m128i d, z, a, b, xt1, vt1, ut, tmp;
__dp_code_block1;
d = _mm_and_si128(_mm_cmpgt_epi8(a, z), flag1_); // d = a > z? 1 : 0
#ifdef __SSE4_1__
z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
tmp = _mm_cmpgt_epi8(b, z);
d = _mm_blendv_epi8(d, flag2_, tmp); // d = b > z? 2 : d
#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
tmp = _mm_cmpgt_epi8(b, z);
d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, flag2_)); // d = b > z? 2 : d; emulating blendv
#endif
__dp_code_block2;
tmp = _mm_cmpgt_epi8(a, zero_);
_mm_store_si128(&x[t], _mm_and_si128(tmp, a));
d = _mm_or_si128(d, _mm_and_si128(tmp, flag8_)); // d = a > 0? 0x08 : 0
tmp = _mm_cmpgt_epi8(b, zero_);
_mm_store_si128(&y[t], _mm_and_si128(tmp, b));
d = _mm_or_si128(d, _mm_and_si128(tmp, flag16_)); // d = b > 0? 0x10 : 0
_mm_store_si128(&pr[t], d);
}
} else { // gap right-alignment
__m128i *pr = p + (size_t)r * n_col_ - st_;
off[r] = st, off_end[r] = en;
for (t = st_; t <= en_; ++t) {
__m128i d, z, a, b, xt1, vt1, ut, tmp;
__dp_code_block1;
d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), flag1_); // d = z > a? 0 : 1
#ifdef __SSE4_1__
z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
tmp = _mm_cmpgt_epi8(z, b);
d = _mm_blendv_epi8(flag2_, d, tmp); // d = z > b? d : 2
#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
tmp = _mm_cmpgt_epi8(z, b);
d = _mm_or_si128(_mm_andnot_si128(tmp, flag2_), _mm_and_si128(tmp, d)); // d = z > b? d : 2; emulating blendv
#endif
__dp_code_block2;
tmp = _mm_cmpgt_epi8(zero_, a);
_mm_store_si128(&x[t], _mm_andnot_si128(tmp, a));
d = _mm_or_si128(d, _mm_andnot_si128(tmp, flag8_)); // d = 0 > a? 0 : 0x08
tmp = _mm_cmpgt_epi8(zero_, b);
_mm_store_si128(&y[t], _mm_andnot_si128(tmp, b));
d = _mm_or_si128(d, _mm_andnot_si128(tmp, flag16_)); // d = 0 > b? 0 : 0x10
_mm_store_si128(&pr[t], d);
}
}
if (!approx_max) { // find the exact max with a 32-bit score array
int32_t max_H, max_t;
// compute H[], max_H and max_t
if (r > 0) {
int32_t HH[4], tt[4], en1 = st0 + (en0 - st0) / 4 * 4, i;
__m128i max_H_, max_t_, qe_;
max_H = H[en0] = en0 > 0? H[en0-1] + u8[en0] - qe : H[en0] + v8[en0] - qe; // special casing the last element
max_t = en0;
max_H_ = _mm_set1_epi32(max_H);
max_t_ = _mm_set1_epi32(max_t);
qe_ = _mm_set1_epi32(q + e);
for (t = st0; t < en1; t += 4) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
__m128i H1, tmp, t_;
H1 = _mm_loadu_si128((__m128i*)&H[t]);
t_ = _mm_setr_epi32(v8[t], v8[t+1], v8[t+2], v8[t+3]);
H1 = _mm_add_epi32(H1, t_);
H1 = _mm_sub_epi32(H1, qe_);
_mm_storeu_si128((__m128i*)&H[t], H1);
t_ = _mm_set1_epi32(t);
tmp = _mm_cmpgt_epi32(H1, max_H_);
#ifdef __SSE4_1__
max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);
max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);
#else
max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));
max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));
#endif
}
_mm_storeu_si128((__m128i*)HH, max_H_);
_mm_storeu_si128((__m128i*)tt, max_t_);
for (i = 0; i < 4; ++i)
if (max_H < HH[i]) max_H = HH[i], max_t = tt[i] + i;
for (; t < en0; ++t) { // for the rest of values that haven't been computed with SSE
H[t] += (int32_t)v8[t] - qe;
if (H[t] > max_H)
max_H = H[t], max_t = t;
}
} else H[0] = v8[0] - qe - qe, max_H = H[0], max_t = 0; // special casing r==0
// update ez
if (en0 == tlen - 1 && H[en0] > ez->mte)
ez->mte = H[en0], ez->mte_q = r - en0;
if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
ez->mqe = H[st0], ez->mqe_t = st0;
if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e)) break;
if (r == qlen + tlen - 2 && en0 == tlen - 1)
ez->score = H[tlen - 1];
} else { // find approximate max; Z-drop might be inaccurate, too.
if (r > 0) {
if (last_H0_t >= st0 && last_H0_t <= en0 && last_H0_t + 1 >= st0 && last_H0_t + 1 <= en0) {
int32_t d0 = v8[last_H0_t] - qe;
int32_t d1 = u8[last_H0_t + 1] - qe;
if (d0 > d1) H0 += d0;
else H0 += d1, ++last_H0_t;
} else if (last_H0_t >= st0 && last_H0_t <= en0) {
H0 += v8[last_H0_t] - qe;
} else {
++last_H0_t, H0 += u8[last_H0_t] - qe;
}
if ((flag & KSW_EZ_APPROX_DROP) && ksw_apply_zdrop(ez, 1, H0, r, last_H0_t, zdrop, e)) break;
} else H0 = v8[0] - qe - qe, last_H0_t = 0;
if (r == qlen + tlen - 2 && en0 == tlen - 1)
ez->score = H0;
}
last_st = st, last_en = en;
//for (t = st0; t <= en0; ++t) printf("(%d,%d)\t(%d,%d,%d,%d)\t%d\n", r, t, ((int8_t*)u)[t], ((int8_t*)v)[t], ((int8_t*)x)[t], ((int8_t*)y)[t], H[t]); // for debugging
}
kfree(km, mem);
if (!approx_max) kfree(km, H);
if (with_cigar) { // backtrack
int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
ez->reach_end = 1;
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (ez->max_t >= 0 && ez->max_q >= 0) {
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
}
kfree(km, mem2); kfree(km, off);
}
}
#endif // __SSE2__