#include #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_exts2_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, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez) #else void ksw_exts2_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, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez) #endif #else void ksw_exts2_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, int8_t q2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez) #endif // ~KSW_CPU_DISPATCH { #define __dp_code_block1 \ z = _mm_load_si128(&s[t]); \ 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] */ \ x2t1= _mm_load_si128(&x2[t]); \ tmp = _mm_srli_si128(x2t1, 15); \ x2t1= _mm_or_si128(_mm_slli_si128(x2t1, 1), x21_); \ x21_= tmp; \ a2 = _mm_add_epi8(x2t1, vt1); \ a2a = _mm_add_epi8(a2, _mm_load_si128(&acceptor[t])); #define __dp_code_block2 \ _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] */ \ tmp = _mm_sub_epi8(z, q_); \ a = _mm_sub_epi8(a, tmp); \ b = _mm_sub_epi8(b, tmp); \ a2= _mm_sub_epi8(a2, _mm_sub_epi8(z, q2_)); int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, max_sc, min_sc, long_thres, long_diff; 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_, q2_, qe_, zero_, sc_mch_, sc_mis_, sc_N_, m1_; __m128i *u, *v, *x, *y, *x2, *s, *p = 0, *donor, *acceptor; ksw_reset_extz(ez); if (m <= 1 || qlen <= 0 || tlen <= 0 || q2 <= q + e) return; zero_ = _mm_set1_epi8(0); q_ = _mm_set1_epi8(q); q2_ = _mm_set1_epi8(q2); qe_ = _mm_set1_epi8(q + e); 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 tlen_ = (tlen + 15) / 16; n_col_ = ((qlen < tlen? qlen : tlen) + 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 long_thres = (q2 - q) / e - 1; if (q2 > q + e + long_thres * e) ++long_thres; long_diff = long_thres * e - (q2 - q); mem = (uint8_t*)kcalloc(km, tlen_ * 9 + qlen_ + 1, 16); u = (__m128i*)(((size_t)mem + 15) >> 4 << 4); // 16-byte aligned v = u + tlen_, x = v + tlen_, y = x + tlen_, x2 = y + tlen_; donor = x2 + tlen_, acceptor = donor + tlen_; s = acceptor + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 16; memset(u, -q - e, tlen_ * 16 * 4); // this set u, v, x, y (because they are in the same array) memset(x2, -q2, 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); // set the donor and acceptor arrays. TODO: this assumes 0/1/2/3 encoding! if (flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) { int semi_cost = flag&KSW_EZ_SPLICE_FLANK? -noncan/2 : 0; // GTr or yAG is worth 0.5 bit; see PMID:18688272 memset(donor, -noncan, tlen_ * 16); memset(acceptor, -noncan, tlen_ * 16); if (!(flag & KSW_EZ_REV_CIGAR)) { for (t = 0; t < tlen - 4; ++t) { int can_type = 0; // type of canonical site: 0=none, 1=GT/AG only, 2=GTr/yAG if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 3) can_type = 1; // GTr... if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 3) can_type = 1; // CTr... if (can_type && (target[t+3] == 0 || target[t+3] == 2)) can_type = 2; if (can_type) ((int8_t*)donor)[t] = can_type == 2? 0 : semi_cost; } if (junc) for (t = 0; t < tlen - 1; ++t) if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&8))) ((int8_t*)donor)[t] += junc_bonus; for (t = 2; t < tlen; ++t) { int can_type = 0; if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 0 && target[t] == 2) can_type = 1; // ...yAG if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 0 && target[t] == 1) can_type = 1; // ...yAC if (can_type && (target[t-2] == 1 || target[t-2] == 3)) can_type = 2; if (can_type) ((int8_t*)acceptor)[t] = can_type == 2? 0 : semi_cost; } if (junc) for (t = 0; t < tlen; ++t) if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&4))) ((int8_t*)acceptor)[t] += junc_bonus; } else { for (t = 0; t < tlen - 4; ++t) { int can_type = 0; // type of canonical site: 0=none, 1=GT/AG only, 2=GTr/yAG if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 0) can_type = 1; // GAy... if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 0) can_type = 1; // CAy... if (can_type && (target[t+3] == 1 || target[t+3] == 3)) can_type = 2; if (can_type) ((int8_t*)donor)[t] = can_type == 2? 0 : semi_cost; } if (junc) for (t = 0; t < tlen - 1; ++t) if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&4))) ((int8_t*)donor)[t] += junc_bonus; for (t = 2; t < tlen; ++t) { int can_type = 0; if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 3 && target[t] == 2) can_type = 1; // ...rTG if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 3 && target[t] == 1) can_type = 1; // ...rTC if (can_type && (target[t-2] == 0 || target[t-2] == 2)) can_type = 2; if (can_type) ((int8_t*)acceptor)[t] = can_type == 2? 0 : semi_cost; } if (junc) for (t = 0; t < tlen; ++t) if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8))) ((int8_t*)acceptor)[t] += junc_bonus; } } 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, x21, v1, *u8 = (int8_t*)u, *v8 = (int8_t*)v; uint8_t *qrr = qr + (qlen - 1 - r); __m128i x1_, x21_, v1_; // find the boundaries if (st < r - qlen + 1) st = r - qlen + 1; if (en > r) en = r; 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 = ((int8_t*)x)[st - 1], x21 = ((int8_t*)x2)[st - 1], v1 = v8[st - 1]; // (r-1,s-1) calculated in the last round else x1 = -q - e, x21 = -q2, v1 = -q - e; } else { x1 = -q - e, x21 = -q2; v1 = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : 0; } if (en >= r) { ((int8_t*)y)[r] = -q - e; u8[r] = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : 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*)((int8_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((uint8_t)x1); x21_ = _mm_cvtsi32_si128((uint8_t)x21); v1_ = _mm_cvtsi32_si128((uint8_t)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, a2, a2a, xt1, x2t1, vt1, ut, tmp; __dp_code_block1; #ifdef __SSE4_1__ z = _mm_max_epi8(z, a); z = _mm_max_epi8(z, b); z = _mm_max_epi8(z, a2a); __dp_code_block2; // save u[] and v[]; update a, b and a2 _mm_store_si128(&x[t], _mm_sub_epi8(_mm_max_epi8(a, zero_), qe_)); _mm_store_si128(&y[t], _mm_sub_epi8(_mm_max_epi8(b, zero_), qe_)); tmp = _mm_load_si128(&donor[t]); _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, tmp), q2_)); #else tmp = _mm_cmpgt_epi8(a, z); z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a)); tmp = _mm_cmpgt_epi8(b, z); z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b)); tmp = _mm_cmpgt_epi8(a2a, z); z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a)); __dp_code_block2; tmp = _mm_cmpgt_epi8(a, zero_); _mm_store_si128(&x[t], _mm_sub_epi8(_mm_and_si128(tmp, a), qe_)); tmp = _mm_cmpgt_epi8(b, zero_); _mm_store_si128(&y[t], _mm_sub_epi8(_mm_and_si128(tmp, b), qe_)); tmp = _mm_load_si128(&donor[t]); // TODO: check if this is correct tmp = _mm_cmpgt_epi8(a2, tmp); tmp = _mm_or_si128(_mm_andnot_si128(tmp, tmp), _mm_and_si128(tmp, a2)); _mm_store_si128(&x2[t], _mm_sub_epi8(tmp, q2_)); #endif } } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment __m128i *pr = p + r * n_col_ - st_; off[r] = st, off_end[r] = en; for (t = st_; t <= en_; ++t) { __m128i d, z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp, tmp2; __dp_code_block1; #ifdef __SSE4_1__ d = _mm_and_si128(_mm_cmpgt_epi8(a, z), _mm_set1_epi8(1)); // d = a > z? 1 : 0 z = _mm_max_epi8(z, a); d = _mm_blendv_epi8(d, _mm_set1_epi8(2), _mm_cmpgt_epi8(b, z)); // d = b > z? 2 : d z = _mm_max_epi8(z, b); d = _mm_blendv_epi8(d, _mm_set1_epi8(3), _mm_cmpgt_epi8(a2a, z)); // d = a2 > z? 3 : d z = _mm_max_epi8(z, a2a); #else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8() tmp = _mm_cmpgt_epi8(a, z); d = _mm_and_si128(tmp, _mm_set1_epi8(1)); z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a)); tmp = _mm_cmpgt_epi8(b, z); d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(2))); z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b)); tmp = _mm_cmpgt_epi8(a2a, z); d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(3))); z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a)); #endif __dp_code_block2; tmp = _mm_cmpgt_epi8(a, zero_); _mm_store_si128(&x[t], _mm_sub_epi8(_mm_and_si128(tmp, a), qe_)); d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x08))); // d = a > 0? 1<<3 : 0 tmp = _mm_cmpgt_epi8(b, zero_); _mm_store_si128(&y[t], _mm_sub_epi8(_mm_and_si128(tmp, b), qe_)); d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x10))); // d = b > 0? 1<<4 : 0 tmp2 = _mm_load_si128(&donor[t]); tmp = _mm_cmpgt_epi8(a2, tmp2); #ifdef __SSE4_1__ tmp2 = _mm_max_epi8(a2, tmp2); #else tmp2 = _mm_or_si128(_mm_andnot_si128(tmp, tmp2), _mm_and_si128(tmp, a2)); #endif _mm_store_si128(&x2[t], _mm_sub_epi8(tmp2, q2_)); d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x20))); _mm_store_si128(&pr[t], d); } } else { // gap right-alignment __m128i *pr = p + r * n_col_ - st_; off[r] = st, off_end[r] = en; for (t = st_; t <= en_; ++t) { __m128i d, z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp, tmp2; __dp_code_block1; #ifdef __SSE4_1__ d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), _mm_set1_epi8(1)); // d = z > a? 0 : 1 z = _mm_max_epi8(z, a); d = _mm_blendv_epi8(_mm_set1_epi8(2), d, _mm_cmpgt_epi8(z, b)); // d = z > b? d : 2 z = _mm_max_epi8(z, b); d = _mm_blendv_epi8(_mm_set1_epi8(3), d, _mm_cmpgt_epi8(z, a2a)); // d = z > a2? d : 3 z = _mm_max_epi8(z, a2a); #else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8() tmp = _mm_cmpgt_epi8(z, a); d = _mm_andnot_si128(tmp, _mm_set1_epi8(1)); z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a)); tmp = _mm_cmpgt_epi8(z, b); d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(2))); z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b)); tmp = _mm_cmpgt_epi8(z, a2a); d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(3))); z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a2a)); #endif __dp_code_block2; tmp = _mm_cmpgt_epi8(zero_, a); _mm_store_si128(&x[t], _mm_sub_epi8(_mm_andnot_si128(tmp, a), qe_)); d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x08))); // d = a > 0? 1<<3 : 0 tmp = _mm_cmpgt_epi8(zero_, b); _mm_store_si128(&y[t], _mm_sub_epi8(_mm_andnot_si128(tmp, b), qe_)); d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x10))); // d = b > 0? 1<<4 : 0 tmp2 = _mm_load_si128(&donor[t]); tmp = _mm_cmpgt_epi8(tmp2, a2); #ifdef __SSE4_1__ tmp2 = _mm_max_epi8(tmp2, a2); #else tmp2 = _mm_or_si128(_mm_andnot_si128(tmp, a2), _mm_and_si128(tmp, tmp2)); #endif _mm_store_si128(&x2[t], _mm_sub_epi8(tmp2, q2_)); d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0 _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_; max_H = H[en0] = en0 > 0? H[en0-1] + u8[en0] : H[en0] + v8[en0]; // special casing the last element max_t = en0; max_H_ = _mm_set1_epi32(max_H); max_t_ = _mm_set1_epi32(max_t); 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_); _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]; if (H[t] > max_H) max_H = H[t], max_t = t; } } else H[0] = v8[0] - 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 - en; 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, 0)) 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]; int32_t d1 = u8[last_H0_t + 1]; 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]; } else { ++last_H0_t, H0 += u8[last_H0_t]; } } else H0 = v8[0] - qe, last_H0_t = 0; if ((flag & KSW_EZ_APPROX_DROP) && ksw_apply_zdrop(ez, 1, H0, r, last_H0_t, zdrop, 0)) break; 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, long_thres, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, 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, long_thres, (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__