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avoid wasted memory allocation for backtrack

This commit is contained in:
Heng Li 2017-08-08 11:29:46 -04:00
parent 0137d0dfab
commit 4badf2fcbf
2 changed files with 8 additions and 2 deletions
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5
ksw2_extd2_sse.c
View File

@ -1,5 +1,6 @@
#include <string.h>
#include <stdio.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
@ -66,7 +67,8 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
if (w < 0) w = tlen > qlen? tlen : qlen;
wl = wr = w;
tlen_ = (tlen + 15) / 16;
n_col_ = ((w + 1 < tlen? (w + 1 < qlen? w + 1 : qlen): tlen) + 15) / 16 + 1;
n_col_ = qlen < tlen? qlen : tlen;
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 15) / 16 + 1;
qlen_ = (qlen + 15) / 16;
for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
max_sc = max_sc > mat[t]? max_sc : mat[t];
@ -161,6 +163,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
x21_ = _mm_cvtsi32_si128((uint8_t)x21);
v1_ = _mm_cvtsi32_si128((uint8_t)v1);
st_ = st / 16, en_ = en / 16;
assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
for (t = st_; t <= en_; ++t) {
__m128i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;

5
ksw2_extz2_sse.c
View File

@ -1,4 +1,5 @@
#include <string.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
@ -58,7 +59,8 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
if (w < 0) w = tlen > qlen? tlen : qlen;
wl = wr = w;
tlen_ = (tlen + 15) / 16;
n_col_ = ((w + 1 < tlen? (w + 1 < qlen? w + 1 : qlen): tlen) + 15) / 16 + 1;
n_col_ = qlen < tlen? qlen : tlen;
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 15) / 16 + 1;
qlen_ = (qlen + 15) / 16;
for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
max_sc = max_sc > mat[t]? max_sc : mat[t];
@ -130,6 +132,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
x1_ = _mm_cvtsi32_si128(x1);
v1_ = _mm_cvtsi32_si128(v1);
st_ = st / 16, en_ = en / 16;
assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
for (t = st_; t <= en_; ++t) {
__m128i z, a, b, xt1, vt1, ut, tmp;