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remove the thresholding version

This commit is contained in:
Heng Li 2011-05-17 21:19:06 -04:00
parent 8f06ff0d47
commit 5c7ada67e8
1 changed files with 9 additions and 20 deletions
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29
ksw.c
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@ -92,9 +92,9 @@ ksw_query_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const in
int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) // the first gap costs -(_o+_e)
{
int slen, i, sum, m_b, n_b, te = -1, gmax = 0, _thres = 254 - q->mdiff;
int slen, i, sum, m_b, n_b, te = -1, gmax = 0;
uint64_t *b;
__m128i zero, gapoe, gape, shift, reduce, thres, *H0, *H1, *E, *Hmax;
__m128i zero, gapoe, gape, shift, reduce, *H0, *H1, *E, *Hmax;
#define __max_16(ret, xx) do { \
(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
@ -110,7 +110,6 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) /
gapoe = _mm_set1_epi8(a->gapo + a->gape);
gape = _mm_set1_epi8(a->gape);
shift = _mm_set1_epi8(q->shift);
thres = _mm_set1_epi8(_thres); // when max score exceeds this, shift all scores by "reduce" below
reduce = _mm_set1_epi8(127);
H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
slen = q->slen;
@ -166,34 +165,24 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) /
end_loop:
//int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&max)[k]);printf("\n");
__max_16(imax, max); // imax is the maximum number in max
if (imax + sum >= a->T) { // write the b array; this condition adds branching unfornately
if (imax >= a->T) { // write the b array; this condition adds branching unfornately
if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append
if (n_b == m_b) {
m_b = m_b? m_b<<1 : 8;
b = realloc(b, 8 * m_b);
}
b[n_b++] = (uint64_t)(imax + sum)<<32 | i;
} else if ((int)(b[n_b-1]>>32) < imax + sum) b[n_b-1] = (uint64_t)(imax + sum)<<32 | i; // modify the last
b[n_b++] = (uint64_t)imax<<32 | i;
} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
}
if (imax > gmax) {
gmax = imax; te = i; // te is the end position on the target
for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
}
if (gmax >= _thres) { // reduce
// When overflow is going to happen, subtract 127 from all scores. This heuristic
// may miss the best alignment, but in practice this should happen very rarely.
sum += 127; gmax -= 127;
for (j = 0; LIKELY(j < slen); ++j) {
h = _mm_subs_epu8(_mm_load_si128(H1 + j), reduce);
_mm_store_si128(H1 + j, h);
e = _mm_subs_epu8(_mm_load_si128(E + j), reduce);
_mm_store_si128(E + j, e);
}
if (gmax + q->shift >= 255) break;
}
S = H1; H1 = H0; H0 = S; // swap H0 and H1
}
a->score = gmax + sum; a->te = te;
a->score = gmax; a->te = te;
{ // get a->qe, the end of query match; find the 2nd best score
int max = -1, low, high, qlen = slen * 16;
uint8_t *t = (uint8_t*)Hmax;
@ -209,7 +198,7 @@ end_loop:
}
}
free(b);
return a->score;
return a->score + q->shift >= 255? 255 : a->score;
}
int ksw_sse2_8(ksw_query_t *q, int tlen, const uint8_t *target, ksw_aux_t *a) // the first gap costs -(_o+_e)
@ -363,7 +352,7 @@ int main(int argc, char *argv[])
}
}
if (optind + 2 > argc) {
fprintf(stderr, "Usage: ksw [-a%d] [-b%d] [-q%d] [-r%d] <target.fa> <query.fa>\n", sa, sb, a.gapo, a.gape);
fprintf(stderr, "Usage: ksw [-s%d] [-a%d] [-b%d] [-q%d] [-r%d] <target.fa> <query.fa>\n", size, sa, sb, a.gapo, a.gape);
return 1;
}
// initialize scoring matrix