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fixed two bugs when computing full score

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This commit is contained in:
Heng Li
2019-01-01 11:46:01 -05:00
parent 6d9ce56721
commit feca68c71d
1 changed files with 9 additions and 9 deletions
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18
ksw2_extd2_avx512.c
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@@ -149,9 +149,9 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
((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);
x1_ = _mm512_maskz_set1_epi8(1, x1);
x21_ = _mm512_maskz_set1_epi8(1, x21);
v1_ = _mm512_maskz_set1_epi8(1, v1);
st_ = st / 64, en_ = en / 64;
assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
@@ -226,27 +226,27 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
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;
int32_t HH[16], tt[16], en1 = st0 + (en0 - st0) / 16 * 16, 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;
for (t = st0; t < en1; t += 16) { // this implements: H[t]+=v8[t]; 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]));
t_ = _mm512_cvtepi8_epi32(_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, max_H_, H1);
max_H_ = _mm512_mask_blend_epi8(tmp2, max_t_, t_);
max_H_ = _mm512_mask_blend_epi32(tmp2, max_H_, H1);
max_t_ = _mm512_mask_blend_epi32(tmp2, max_t_, t_);
}
_mm512_storeu_si512((__m512i*)HH, max_H_);
_mm512_storeu_si512((__m512i*)tt, max_t_);
for (i = 0; i < 64/4; ++i)
for (i = 0; i < 16; ++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];