#include #include #include "ksw2.h" #ifdef __SSE2__ #ifdef USE_SIMDE #include #else #include #endif #ifdef KSW_SSE2_ONLY #undef __SSE4_1__ #endif #ifdef __SSE4_1__ #ifdef USE_SIMDE #include #else #include #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__