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backup: preliminary boundary alignment

This commit is contained in:
Heng Li 2017-08-12 23:10:14 -04:00
parent bcfe00d2ad
commit 43506edbc5
5 changed files with 70 additions and 38 deletions
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2
align.c
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@ -136,7 +136,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); fputc('\n', stderr);
}
if (opt->flag & MM_F_SPLICE)
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->zdrop, flag, ez);
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, opt->zdrop, flag|KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, opt->zdrop, flag, ez);
else

4
ksw2.h
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@ -12,6 +12,8 @@
#define KSW_EZ_APPROX_DROP 0x10 // approximate Z-drop; faster with sse
#define KSW_EZ_EXTZ_ONLY 0x40 // only perform extension
#define KSW_EZ_REV_CIGAR 0x80 // reverse CIGAR in the output
#define KSW_EZ_SPLICE_FOR 0x100
#define KSW_EZ_SPLICE_REV 0x200
#ifdef __cplusplus
extern "C" {
@ -54,7 +56,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int flag, ksw_extz_t *ez);
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 gapo, int8_t gape, int8_t gapo2, int zdrop, int flag, ksw_extz_t *ez);
int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
void ksw_extf2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez);

100
ksw2_exts2_sse.c
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@ -11,7 +11,7 @@
#endif
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, int zdrop, int flag, ksw_extz_t *ez)
int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
{
#define __dp_code_block1 \
z = _mm_load_si128(&s[t]); \
@ -30,7 +30,8 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
tmp = _mm_srli_si128(x2t1, 15); \
x2t1= _mm_or_si128(_mm_slli_si128(x2t1, 1), x21_); \
x21_= tmp; \
a2= _mm_add_epi8(x2t1, vt1);
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] */ \
@ -45,7 +46,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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_, m1_;
__m128i *u, *v, *x, *y, *x2, *s, *p = 0;
__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;
@ -72,10 +73,11 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
++long_thres;
long_diff = long_thres * e - (q2 - q);
mem = (uint8_t*)kcalloc(km, tlen_ * 7 + qlen_ + 1, 16);
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_;
s = x2 + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 16;
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) {
@ -92,6 +94,24 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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)) {
memset(donor, -noncan, tlen_ * 16);
for (t = 0; t < tlen - 2; ++t) {
int is_can = 0; // is a canonical site
if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 3) is_can = 1;
if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 3) is_can = 1;
if (is_can) ((int8_t*)donor)[t] = 0;
}
memset(acceptor, -noncan, tlen_ * 16);
for (t = 2; t < tlen; ++t) {
int is_can = 0;
if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 0 && target[t] == 2) is_can = 1;
if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 0 && target[t] == 1) is_can = 1;
if (is_can) ((int8_t*)acceptor)[t] = 0;
}
}
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;
@ -143,49 +163,48 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
for (t = st_; t <= en_; ++t) {
__m128i z, a, b, a2, xt1, x2t1, vt1, ut, tmp;
__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, a2);
z = _mm_min_epi8(z, sc_mch_);
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_));
_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, zero_), q2_));
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(a2, z);
z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2));
tmp = _mm_cmplt_epi8(sc_mch_, z);
z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
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_cmpgt_epi8(a2, zero_);
_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_and_si128(tmp, a2), q2_));
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, xt1, x2t1, vt1, ut, tmp;
__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(a2, z)); // d = a2 > z? 3 : d
z = _mm_max_epi8(z, a2);
z = _mm_min_epi8(z, sc_mch_);
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));
@ -193,11 +212,9 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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);
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, a2));
tmp = _mm_cmplt_epi8(sc_mch_, z);
z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a));
#endif
__dp_code_block2;
tmp = _mm_cmpgt_epi8(a, zero_);
@ -206,25 +223,31 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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), q2_));
d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 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, xt1, x2t1, vt1, ut, tmp;
__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, a2)); // d = z > a2? d : 3
z = _mm_max_epi8(z, a2);
z = _mm_min_epi8(z, sc_mch_);
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));
@ -232,11 +255,9 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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);
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, a2));
tmp = _mm_cmplt_epi8(sc_mch_, z);
z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a2a));
#endif
__dp_code_block2;
tmp = _mm_cmpgt_epi8(zero_, a);
@ -245,8 +266,15 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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), q2_));
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);
}

1
main.c
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@ -142,6 +142,7 @@ int main(int argc, char *argv[])
opt.flag |= MM_F_SPLICE;
opt.max_gap = 2000, opt.max_gap_ref = opt.bw = 200000;
opt.a = 1, opt.b = 2, opt.q = 2, opt.e = 1, opt.q2 = 32, opt.e2 = 0;
opt.noncan = 4;
opt.zdrop = 200;
} else {
fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);

1
minimap.h
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@ -94,6 +94,7 @@ typedef struct {
int min_join_flank_sc;
int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
int noncan;
int zdrop;
int min_dp_max;
int min_ksw_len;