diff --git a/Makefile b/Makefile index ee7bd8e..b5fb136 100644 --- a/Makefile +++ b/Makefile @@ -2,16 +2,21 @@ CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra CPPFLAGS= -DHAVE_KALLOC INCLUDES= OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o +OBJS_SSE= ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o PROG= minimap2 PROG_EXTRA= sdust minimap2-lite LIBS= -lm -lz -lpthread ifeq ($(arm_neon),) # if arm_neon is not defined ifeq ($(sse2only),) # if sse2only is not defined +ifeq ($(avx512),) ifeq ($(avx2),) - OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o + OBJS+=$(OBJS_SSE) ksw2_dispatch.o else - OBJS+=ksw2_extd2_avx2.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o + OBJS+=ksw2_extd2_avx2.o $(OBJS_SSE) ksw2_dispatch.o +endif +else + OBJS+=ksw2_extd2_avx512.o ksw2_extd2_avx2.o $(OBJS_SSE) ksw2_dispatch.o endif else # if sse2only is defined OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o @@ -64,6 +69,9 @@ ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h ksw2_extd2_avx2.o:ksw2_extd2_sse.c ksw2.h kalloc.h $(CC) -c $(CFLAGS) -mavx2 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ +ksw2_extd2_avx512.o:ksw2_extd2_avx512.c ksw2.h kalloc.h + $(CC) -c $(CFLAGS) -mavx512bw $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ + ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h $(CC) -c $(CFLAGS) -msse4.1 -mno-avx2 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ diff --git a/ksw2_dispatch.c b/ksw2_dispatch.c index 79bf191..4512639 100644 --- a/ksw2_dispatch.c +++ b/ksw2_dispatch.c @@ -2,15 +2,16 @@ #include #include "ksw2.h" -#define SIMD_SSE 0x1 -#define SIMD_SSE2 0x2 -#define SIMD_SSE3 0x4 -#define SIMD_SSSE3 0x8 -#define SIMD_SSE4_1 0x10 -#define SIMD_SSE4_2 0x20 -#define SIMD_AVX 0x40 -#define SIMD_AVX2 0x80 -#define SIMD_AVX512F 0x100 +#define SIMD_SSE 0x1 +#define SIMD_SSE2 0x2 +#define SIMD_SSE3 0x4 +#define SIMD_SSSE3 0x8 +#define SIMD_SSE4_1 0x10 +#define SIMD_SSE4_2 0x20 +#define SIMD_AVX 0x40 +#define SIMD_AVX2 0x80 +#define SIMD_AVX512F 0x100 +#define SIMD_AVX512BW 0x200 #ifndef _MSC_VER // adapted from https://github.com/01org/linux-sgx/blob/master/common/inc/internal/linux/cpuid_gnu.h @@ -48,6 +49,7 @@ static int x86_simd(void) __cpuidex(cpuid, 7, 0); if (cpuid[1]>>5 &1) flag |= SIMD_AVX2; if (cpuid[1]>>16&1) flag |= SIMD_AVX512F; + if (cpuid[1]>>30&1) flag |= SIMD_AVX512BW; } return flag; } @@ -73,8 +75,15 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez); extern void ksw_extd2_avx2(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 e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez); + extern void ksw_extd2_avx512(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 e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez); if (ksw_simd < 0) ksw_simd = x86_simd(); -#ifdef __AVX2__ +#if defined(__AVX512BW__) + if (ksw_simd & SIMD_AVX512BW) + ksw_extd2_avx512(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez); + else +#endif +#if defined(__AVX2__) if (ksw_simd & SIMD_AVX2) ksw_extd2_avx2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez); else diff --git a/ksw2_extd2_avx512.c b/ksw2_extd2_avx512.c new file mode 100644 index 0000000..ed3bab3 --- /dev/null +++ b/ksw2_extd2_avx512.c @@ -0,0 +1,300 @@ +#include +#include +#include +#include "ksw2.h" + +#ifdef __AVX512BW__ +#include + +void ksw_extd2_avx512(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 e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez) +{ +#define __dp_code_block1 \ + z = _mm512_load_si512(&s[t]); \ + tmp = _mm512_loadu_si512((uint8_t*)&x[t] - 1); \ + xt1 = _mm512_mask_blend_epi8(1, x1_, tmp); \ + x1_ = _mm512_maskz_mov_epi8(1, tmp); \ + tmp = _mm512_loadu_si512((uint8_t*)&v[t] - 1); \ + vt1 = _mm512_mask_blend_epi8(1, v1_, tmp); \ + v1_ = _mm512_maskz_mov_epi8(1, tmp); \ + a = _mm512_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+62] + v[r-1][t-1..t+62] */ \ + ut = _mm512_load_si512(&u[t]); /* ut <- u[t..t+63] */ \ + b = _mm512_add_epi8(_mm512_load_si512(&y[t]), ut); /* b <- y[r-1][t..t+63] + u[r-1][t..t+63] */ \ + tmp = _mm512_loadu_si512((uint8_t*)&x2[t] - 1); \ + x2t1 = _mm512_mask_blend_epi8(1, x21_, tmp); \ + x21_ = _mm512_maskz_mov_epi8(1, tmp); \ + a2= _mm512_add_epi8(x2t1, vt1); \ + b2= _mm512_add_epi8(_mm512_load_si512(&y2[t]), ut); + +#define __dp_code_block2 \ + _mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));/* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \ + _mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \ + tmp = _mm512_sub_epi8(z, q_); \ + a = _mm512_sub_epi8(a, tmp); \ + b = _mm512_sub_epi8(b, tmp); \ + tmp = _mm512_sub_epi8(z, q2_); \ + a2= _mm512_sub_epi8(a2, tmp); \ + b2= _mm512_sub_epi8(b2, tmp); + + 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, 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; + __m512i q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_; + __m512i *u, *v, *x, *y, *x2, *y2, *s, *p = 0; + + ksw_reset_extz(ez); + if (m <= 1 || qlen <= 0 || tlen <= 0) return; + + if (q2 + e2 < q + e) t = q, q = q2, q2 = t, t = e, e = e2, e2 = t; // make sure q+e no larger than q2+e2 + + zero_ = _mm512_set1_epi8(0); + q_ = _mm512_set1_epi8(q); + q2_ = _mm512_set1_epi8(q2); + qe_ = _mm512_set1_epi8(q + e); + qe2_ = _mm512_set1_epi8(q2 + e2); + sc_mch_ = _mm512_set1_epi8(mat[0]); + sc_mis_ = _mm512_set1_epi8(mat[1]); + sc_N_ = mat[m*m-1] == 0? _mm512_set1_epi8(-e2) : _mm512_set1_epi8(mat[m*m-1]); + m1_ = _mm512_set1_epi8(m - 1); // wildcard + + if (w < 0) w = tlen > qlen? tlen : qlen; + wl = wr = w; + tlen_ = (tlen + 64 - 1) / 64; + n_col_ = qlen < tlen? qlen : tlen; + n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 64 - 1) / 64 + 1; + qlen_ = (qlen + 64 - 1) / 64; + 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 = e != e2? (q2 - q) / (e - e2) - 1 : 0; + if (q2 + e2 + long_thres * e2 > q + e + long_thres * e) + ++long_thres; + long_diff = long_thres * (e - e2) - (q2 - q) - e2; + + mem = (uint8_t*)kcalloc(km, tlen_ * 8 + qlen_ + 1, 64); + u = (__m512i*)(((size_t)mem + 64 - 1) >> 6 << 6); // 16-byte aligned + v = u + tlen_, x = v + tlen_, y = x + tlen_, x2 = y + tlen_, y2 = x2 + tlen_; + s = y2 + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 64; + memset(u, -q - e, tlen_ * 64); + memset(v, -q - e, tlen_ * 64); + memset(x, -q - e, tlen_ * 64); + memset(y, -q - e, tlen_ * 64); + memset(x2, -q2 - e2, tlen_ * 64); + memset(y2, -q2 - e2, tlen_ * 64); + if (!approx_max) { + H = (int32_t*)kmalloc(km, tlen_ * 64 * 4); + for (t = 0; t < tlen_ * 64; ++t) H[t] = KSW_NEG_INF; + } + if (with_cigar) { + mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 64); + p = (__m512i*)(((size_t)mem2 + 64 - 1) >> 6 << 6); + 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, x21, v1; + uint8_t *qrr = qr + (qlen - 1 - r); + int8_t *u8 = (int8_t*)u, *v8 = (int8_t*)v, *x8 = (int8_t*)x, *x28 = (int8_t*)x2; + __m512i x1_, x21_, 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 / 64 * 64, en = (en + 64) / 64 * 64 - 1; + // set boundary conditions + if (st > 0) { + if (st - 1 >= last_st && st - 1 <= last_en) { + x1 = x8[st - 1], x21 = x28[st - 1], v1 = v8[st - 1]; // (r-1,s-1) calculated in the last round + } else { + x1 = -q - e, x21 = -q2 - e2; + v1 = -q - e; + } + } else { + x1 = -q - e, x21 = -q2 - e2; + v1 = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : -e2; + } + if (en >= r) { + ((int8_t*)y)[r] = -q - e, ((int8_t*)y2)[r] = -q2 - e2; + u8[r] = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : -e2; + } + // loop fission: set scores first + if (!(flag & KSW_EZ_GENERIC_SC)) { + for (t = st0; t <= en0; t += 64) { + __m512i sq, st, tmp; + __mmask64 mask; + sq = _mm512_loadu_si512((__m512i*)&sf[t]); + st = _mm512_loadu_si512((__m512i*)&qrr[t]); + mask = _mm512_cmpeq_epi8_mask(sq, m1_) | _mm512_cmpeq_epi8_mask(st, m1_); + tmp = _mm512_mask_blend_epi8(_mm512_cmpeq_epi8_mask(sq, st), sc_mch_, sc_mis_); + tmp = _mm512_mask_blend_epi8(mask, sc_N_, tmp); + _mm512_storeu_si512((__m512i*)((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_ = _mm512_maskz_set1_epi8(1, (uint8_t)x1); + x21_ = _mm512_maskz_set1_epi8(1, (uint8_t)x21); + v1_ = _mm512_maskz_set1_epi8(1, (uint8_t)v1); + st_ = st / 64, en_ = en / 64; + assert(en_ - st_ + 1 <= n_col_); + if (!with_cigar) { // score only + for (t = st_; t <= en_; ++t) { + __m512i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp; + __dp_code_block1; + z = _mm512_max_epi8(z, a); + z = _mm512_max_epi8(z, b); + z = _mm512_max_epi8(z, a2); + z = _mm512_max_epi8(z, b2); + z = _mm512_min_epi8(z, sc_mch_); + __dp_code_block2; // save u[] and v[]; update a, b, a2 and b2 + _mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_)); + _mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_)); + _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe_)); + _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe_)); + } + } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment + __m512i *pr = p + (size_t)r * n_col_ - st_; + off[r] = st, off_end[r] = en; + for (t = st_; t <= en_; ++t) { + __m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp; + __dp_code_block1; + d = _mm512_mask_blend_epi8(_mm512_cmplt_epi8_mask(a, z), _mm512_set1_epi8(1), zero_); + z = _mm512_max_epi8(z, a); + d = _mm512_mask_blend_epi8(_mm512_cmplt_epi8_mask(b, z), _mm512_set1_epi8(2), d); + z = _mm512_max_epi8(z, b); + d = _mm512_mask_blend_epi8(_mm512_cmplt_epi8_mask(a2, z), _mm512_set1_epi8(3), d); + z = _mm512_max_epi8(z, a2); + d = _mm512_mask_blend_epi8(_mm512_cmplt_epi8_mask(b2, z), _mm512_set1_epi8(4), d); + z = _mm512_max_epi8(z, b2); + z = _mm512_min_epi8(z, sc_mch_); + __dp_code_block2; + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(a, zero_), 0x08)); // d = a > 0? 1<<3 : 0 + _mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_)); + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(b, zero_), 0x10)); // d = b > 0? 1<<4 : 0 + _mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_)); + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(a2, zero_), 0x20)); // d = a2 > 0? 1<<5 : 0 + _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe_)); + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(b2, zero_), 0x40)); // d = b2 > 0? 1<<6 : 0 + _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe_)); + _mm512_store_si512(&pr[t], d); + } + } else { // gap right-alignment + __m512i *pr = p + (size_t)r * n_col_ - st_; + off[r] = st, off_end[r] = en; + for (t = st_; t <= en_; ++t) { + __m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp; + __dp_code_block1; + d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a), _mm512_setzero(), _mm512_set1_epi8(1)); + z = _mm512_max_epi8(z, a); + d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), d, _mm512_set1_epi8(2)); + z = _mm512_max_epi8(z, b); + d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a2), d, _mm512_set1_epi8(3)); + z = _mm512_max_epi8(z, a2); + d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b2), d, _mm512_set1_epi8(4)); + z = _mm512_max_epi8(z, b2); + z = _mm512_min_epi8(z, sc_mch_); + __dp_code_block2; + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(a, zero_), 0x08)); // d = a >= 0? 1<<3 : 0 + _mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_)); + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(b, zero_), 0x10)); // d = b >= 0? 1<<4 : 0 + _mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_)); + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(a2, zero_), 0x20)); // d = a2 >= 0? 1<<5 : 0 + _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe_)); + d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(b2, zero_), 0x40)); // d = b2 >= 0? 1<<6 : 0 + _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe_)); + _mm512_store_si512(&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[64/4], tt[64/4], en1 = st0 + (en0 - st0) / (64/4) * (64/4), i; + __m512i 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_ = _mm512_set1_epi32(max_H); + max_t_ = _mm512_set1_epi32(max_t); + for (t = st0; t < en1; t += 64/4) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t; + __m512i H1, t_; + __mmask64 tmp2; + H1 = _mm512_loadu_si512((__m512i*)&H[t]); + t_ = _mm512_broadcastb_epi8(_mm_loadu_si128((__m128i*)&v8[t])); + H1 = _mm512_add_epi32(H1, t_); + _mm512_storeu_si512((__m512i*)&H[t], H1); + t_ = _mm512_set1_epi32(t); + tmp2 = _mm512_cmpgt_epi32_mask(H1, max_H_); + max_H_ = _mm512_mask_blend_epi8(tmp2, H1, max_H_); + max_H_ = _mm512_mask_blend_epi8(tmp2, t_, max_t_); + } + _mm512_storeu_si512((__m512i*)HH, max_H_); + _mm512_storeu_si512((__m512i*)tt, max_t_); + for (i = 0; i < 64/4; ++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, e2)) 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, e2)) 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, 0, (uint8_t*)p, off, off_end, n_col_*64, 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_*64, 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_*64, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar); + } + kfree(km, mem2); kfree(km, off); + } +} +#endif // __AVX512BW__