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exts2 working

This commit is contained in:
Heng Li 2017-08-12 19:06:59 -04:00
parent 61eef0575c
commit 17c19e5819
1 changed files with 12 additions and 4 deletions
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16
ksw2_exts2_sse.c
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@ -97,9 +97,8 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
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;
int8_t x1, x21, v1, *u8 = (int8_t*)u, *v8 = (int8_t*)v;
uint8_t *qrr = qr + (qlen - 1 - r);
int8_t *u8 = (int8_t*)u, *v8 = (int8_t*)v;
__m128i x1_, x21_, v1_;
// find the boundaries
if (st < r - qlen + 1) st = r - qlen + 1;
@ -107,8 +106,17 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
st0 = st, en0 = en;
st = st / 16 * 16, en = (en + 16) / 16 * 16 - 1;
// set boundary conditions
x1 = -q - e, x21 = -q2;
v1 = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : 0;
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;