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fixed invalid backtracking, a temporary solution

This commit is contained in:
Heng Li 2017-06-28 18:17:57 -04:00
parent a25866c25c
commit 5e202afb5f
2 changed files with 16 additions and 2 deletions
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1
ksw2.h
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@ -99,7 +99,6 @@ static inline void ksw_backtrack(void *km, int is_rot, int is_rev, const uint8_t
if (is_rot) r = i + j, tmp = p[r * n_col + i - off[r]]; if (is_rot) r = i + j, tmp = p[r * n_col + i - off[r]];
else tmp = p[i * n_col + j - off[i]]; else tmp = p[i * n_col + j - off[i]];
which = tmp >> (which << 1) & 3; which = tmp >> (which << 1) & 3;
if (which == 0 && tmp>>6) break;
if (which == 0) which = tmp & 3; if (which == 0) which = tmp & 3;
if (which == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match if (which == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match
else if (which == 1) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion else if (which == 1) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion

17
ksw2_extz2_sse.c
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@ -95,7 +95,7 @@ void ksw_extz2_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) { for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {
int st = 0, en = tlen - 1, st0, en0, st_, en_; int st = 0, en = tlen - 1, st0, en0, st_, en_;
int8_t x1, v1; int8_t x1, v1;
uint8_t *qrr = qr + (qlen - 1 - r), *u8 = (uint8_t*)u, *v8 = (uint8_t*)v; uint8_t *qrr = qr + (qlen - 1 - r), *u8 = (uint8_t*)u, *v8 = (uint8_t*)v, *x8 = (uint8_t*)x, p_en0 = 0;
__m128i x1_, v1_; __m128i x1_, v1_;
// find the boundaries // find the boundaries
if (st < r - qlen + 1) st = r - qlen + 1; if (st < r - qlen + 1) st = r - qlen + 1;
@ -163,6 +163,13 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
__m128i *pr = p + r * n_col_ - st_; __m128i *pr = p + r * n_col_ - st_;
off[r] = st; off[r] = st;
if (en0 < r) { // to avoid backtracking out of the band; this assumes a fixed band
int8_t a, z = ((uint8_t*)s)[en0] + 2 * qe;
a = x8[en0-1] + v8[en0-1];
p_en0 = a > z? 1 : 0;
z = a > z? a : z;
p_en0 |= a - (z - q) > 0? 1<<2 : 0;
}
for (t = st_; t <= en_; ++t) { for (t = st_; t <= en_; ++t) {
__m128i d, z, a, b, xt1, vt1, ut, tmp; __m128i d, z, a, b, xt1, vt1, ut, tmp;
__dp_code_block1; __dp_code_block1;
@ -189,6 +196,13 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
} else { // gap right-alignment } else { // gap right-alignment
__m128i *pr = p + r * n_col_ - st_; __m128i *pr = p + r * n_col_ - st_;
off[r] = st; off[r] = st;
if (en0 < r) {
int8_t a, z = ((uint8_t*)s)[en0] + 2 * qe;
a = x8[en0-1] + v8[en0-1];
p_en0 = a >= z? 1 : 0;
z = a >= z? a : z;
p_en0 |= a - (z - q) >= 0? 1<<2 : 0;
}
for (t = st_; t <= en_; ++t) { for (t = st_; t <= en_; ++t) {
__m128i d, z, a, b, xt1, vt1, ut, tmp; __m128i d, z, a, b, xt1, vt1, ut, tmp;
__dp_code_block1; __dp_code_block1;
@ -213,6 +227,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
_mm_store_si128(&pr[t], d); _mm_store_si128(&pr[t], d);
} }
} }
if (with_cigar && en0 < r) ((uint8_t*)(p + r * n_col_))[en0 - st] = p_en0;
if (!approx_max) { // find the exact max with a 32-bit score array if (!approx_max) { // find the exact max with a 32-bit score array
int32_t max_H, max_t; int32_t max_H, max_t;
// compute H[], max_H and max_t // compute H[], max_H and max_t