fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-06 05:28:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

minor equivalent changes

Browse Source
This commit is contained in:
Heng Li
2018-12-30 23:15:07 -05:00
parent 9462da5159
commit 2a7d071e8b
1 changed files with 10 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
ksw2_extd2_sse.c
+10 -10
View File
@@ -81,7 +81,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX); 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; int32_t *H = 0, H0 = 0, last_H0_t = 0;
uint8_t *qr, *sf, *mem, *mem2 = 0; uint8_t *qr, *sf, *mem, *mem2 = 0;
SIMD_INT q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_; SIMD_INT q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_, mask1_;
SIMD_INT *u, *v, *x, *y, *x2, *y2, *s, *p = 0; SIMD_INT *u, *v, *x, *y, *x2, *y2, *s, *p = 0;
ksw_reset_extz(ez); ksw_reset_extz(ez);
@@ -99,6 +99,12 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
sc_N_ = mat[m*m-1] == 0? simd_func(set1_epi8)(-e2) : simd_func(set1_epi8)(mat[m*m-1]); sc_N_ = mat[m*m-1] == 0? simd_func(set1_epi8)(-e2) : simd_func(set1_epi8)(mat[m*m-1]);
m1_ = simd_func(set1_epi8)(m - 1); // wildcard m1_ = simd_func(set1_epi8)(m - 1); // wildcard
#if defined(__AVX2__)
mask1_ = _mm256_setr_epi32(0xff, 0, 0, 0, 0, 0, 0, 0);
#elif defined(__SSE2__)
mask1_ = _mm_setr_epi32(0xff, 0, 0, 0);
#endif
if (w < 0) w = tlen > qlen? tlen : qlen; if (w < 0) w = tlen > qlen? tlen : qlen;
wl = wr = w; wl = wr = w;
tlen_ = (tlen + SIMD_WIDTH - 1) / SIMD_WIDTH; tlen_ = (tlen + SIMD_WIDTH - 1) / SIMD_WIDTH;
@@ -195,15 +201,9 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]]; ((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
} }
// core loop // core loop
#if defined(__AVX2__) x1_ = simd_funcw(and)(simd_func(set1_epi8)((uint8_t)x1), mask1_);
x1_ = _mm256_setr_epi32((uint8_t)x1, 0, 0, 0, 0, 0, 0, 0); x21_ = simd_funcw(and)(simd_func(set1_epi8)((uint8_t)x21), mask1_);
x21_ = _mm256_setr_epi32((uint8_t)x21, 0, 0, 0, 0, 0, 0, 0); v1_ = simd_funcw(and)(simd_func(set1_epi8)((uint8_t)v1), mask1_);
v1_ = _mm256_setr_epi32((uint8_t)v1, 0, 0, 0, 0, 0, 0, 0);
#elif defined(__SSE2__)
x1_ = _mm_setr_epi32((uint8_t)x1, 0, 0, 0);
x21_ = _mm_setr_epi32((uint8_t)x21, 0, 0, 0);
v1_ = _mm_setr_epi32((uint8_t)v1, 0, 0, 0);
#endif
st_ = st / SIMD_WIDTH, en_ = en / SIMD_WIDTH; st_ = st / SIMD_WIDTH, en_ = en / SIMD_WIDTH;
assert(en_ - st_ + 1 <= n_col_); assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only if (!with_cigar) { // score only