minibwa 0.0.0

data/ext/minibwa/minibwa/ksw2_extd2_sse.c

@@ -0,0 +1,403 @@
+#include <string.h>
+#include <assert.h>
+#include "ksw2.h"
+
+#if defined(__ARM_NEON)
+#define __SSE4_1__
+#include "s2n-lite.h"
+#elif defined(__SSE4_1__)
+#include <smmintrin.h>
+#elif defined(__SSE2__)
+#include <xmmintrin.h>
+#else
+#error "Missing SSE2 or NEON intrinsics"
+#endif
+
+static inline __m128i ksw_i8x4_to_i32x4(const int8_t *x)
+{
+#if defined(__ARM_NEON)
+    return vreinterpretq_u8_s32(vmovl_s16(vget_low_s16(vmovl_s8(vcreate_s8((uint64_t)(uint32_t)*(int32_t*)x)))));
+#elif defined(__SSE4_1__)
+	return _mm_cvtepi8_epi32(_mm_cvtsi32_si128(*(int32_t*)x));
+#else
+	return _mm_setr_epi32(x[0], x[1], x[2], x[3]);
+#endif
+}
+
+void ksw_extd2_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 e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
+{
+#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); \
+	b2= _mm_add_epi8(_mm_load_si128(&y2[t]), ut);
+
+#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); \
+	tmp = _mm_sub_epi8(z, q2_); \
+	a2= _mm_sub_epi8(a2, tmp); \
+	b2= _mm_sub_epi8(b2, tmp);
+
+	int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, last_max_H = 0, 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;
+	__m128i q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_;
+	__m128i *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_   = _mm_set1_epi8(0);
+	q_      = _mm_set1_epi8(q);
+	q2_     = _mm_set1_epi8(q2);
+	qe_     = _mm_set1_epi8(q + e);
+	qe2_    = _mm_set1_epi8(q2 + e2);
+	sc_mch_ = _mm_set1_epi8(mat[0]);
+	sc_mis_ = _mm_set1_epi8(mat[1]);
+	sc_N_   = mat[m*m-1] == 0? _mm_set1_epi8(-e2) : _mm_set1_epi8(mat[m*m-1]);
+	m1_     = _mm_set1_epi8(m - 1); // wildcard
+
+	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
+
+	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, 16);
+	u = (__m128i*)(((size_t)mem + 15) >> 4 << 4); // 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_ * 16;
+	memset(u,  -q  - e,  tlen_ * 16);
+	memset(v,  -q  - e,  tlen_ * 16);
+	memset(x,  -q  - e,  tlen_ * 16);
+	memset(y,  -q  - e,  tlen_ * 16);
+	memset(x2, -q2 - e2, tlen_ * 16);
+	memset(y2, -q2 - e2, 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, 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;
+		__m128i 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 / 16 * 16, en = (en + 16) / 16 * 16 - 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 += 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, b2, 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, a2);
+				z = _mm_max_epi8(z, b2);
+				z = _mm_min_epi8(z, sc_mch_);
+				__dp_code_block2; // save u[] and v[]; update a, b, a2 and b2
+				_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_));
+				_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, zero_), qe2_));
+				_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_max_epi8(b2, zero_), qe2_));
+#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(a2, z);
+				z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2));
+				tmp = _mm_cmpgt_epi8(b2, z);
+				z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));
+				tmp = _mm_cmplt_epi8(sc_mch_, z);
+				z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
+				__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_cmpgt_epi8(a2, zero_);
+				_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_and_si128(tmp, a2), qe2_));
+				tmp = _mm_cmpgt_epi8(b2, zero_);
+				_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_and_si128(tmp, b2), qe2_));
+#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, a2, b2, xt1, x2t1, vt1, ut, tmp;
+				__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(a2, z)); // d = a2 > z? 3 : d
+				z = _mm_max_epi8(z, a2);
+				d = _mm_blendv_epi8(d, _mm_set1_epi8(4), _mm_cmpgt_epi8(b2, z)); // d = a2 > z? 3 : d
+				z = _mm_max_epi8(z, b2);
+				z = _mm_min_epi8(z, sc_mch_);
+#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(a2, 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, a2));
+				tmp = _mm_cmpgt_epi8(b2, z);
+				d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, _mm_set1_epi8(4)));
+				z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));
+				tmp = _mm_cmplt_epi8(sc_mch_, z);
+				z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
+#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
+				tmp = _mm_cmpgt_epi8(a2, zero_);
+				_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_and_si128(tmp, a2), qe2_));
+				d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0
+				tmp = _mm_cmpgt_epi8(b2, zero_);
+				_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_and_si128(tmp, b2), qe2_));
+				d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x40))); // d = b > 0? 1<<6 : 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, a2, b2, xt1, x2t1, vt1, ut, tmp;
+				__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, a2)); // d = z > a2? d : 3
+				z = _mm_max_epi8(z, a2);
+				d = _mm_blendv_epi8(_mm_set1_epi8(4), d, _mm_cmpgt_epi8(z, b2)); // d = z > b2? d : 4
+				z = _mm_max_epi8(z, b2);
+				z = _mm_min_epi8(z, sc_mch_);
+#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, a2);
+				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, a2));
+				tmp = _mm_cmpgt_epi8(z, b2);
+				d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(4)));
+				z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b2));
+				tmp = _mm_cmplt_epi8(sc_mch_, z);
+				z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
+#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
+				tmp = _mm_cmpgt_epi8(zero_, a2);
+				_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_andnot_si128(tmp, a2), qe2_));
+				d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0
+				tmp = _mm_cmpgt_epi8(zero_, b2);
+				_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_andnot_si128(tmp, b2), qe2_));
+				d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x40))); // d = b > 0? 1<<6 : 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_, t_, t4_ = _mm_set1_epi32(4);
+				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);
+				t_ = _mm_set1_epi32(st0);
+				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, v_;
+					H1 = _mm_loadu_si128((__m128i*)&H[t]);
+					v_ = ksw_i8x4_to_i32x4(&v8[t]);
+					H1 = _mm_add_epi32(H1, v_);
+					_mm_storeu_si128((__m128i*)&H[t], H1);
+					tmp = _mm_cmpgt_epi32(H1, max_H_);
+#ifdef __SSE4_1__
+					max_H_ = _mm_max_epi32(max_H_, H1);
+					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
+					t_ = _mm_add_epi32(t_, t4_);
+				}
+				_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 - 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, e2)) break;
+			if (r == qlen + tlen - 2 && en0 == tlen - 1)
+				ez->score = H[tlen - 1];
+			// early stopping in the extension-only mode; this block should not change the alignment
+			if (flag & KSW_EZ_EXTZ_ONLY) {
+				int32_t rH = last_max_H > max_H? last_max_H : max_H; // NB: if diagonal r is on the optimal path, r-1 or r+1 is not on the optimal path
+				int32_t rq = qlen - (r - st0), rt = tlen - en0;
+				// 3 conditions: hitting bottom of the DP matrix, hitting the right boundary of the matrix, and bracketing the diagonal
+				int32_t rm = rq >= tlen - st0? tlen - st0 : rt >= qlen - (r - en0)? qlen - (r - en0) : tlen + qlen - 1 - r;
+				if (rH + rm * max_sc + end_bonus < ez->max) break;
+			}
+			last_max_H = max_H; // need this for calculating rH
+		} 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_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
+		} else if ((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);
+	}
+}