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r77: fixed an index loading bug (offset not set)

This commit is contained in:
Heng Li 2017-06-26 13:56:25 -04:00
parent 10644f2165
commit de54c9dac2
5 changed files with 19 additions and 12 deletions
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24
align.c
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@ -170,9 +170,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_seq_rev(qs - qs0, qseq);
mm_seq_rev(rs - rs0, tseq);
ksw_extz2_sse(km, qs - qs0, qseq, rs - rs0, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 1);
r->p->score += ez->max;
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 1);
r->p->score += ez->max;
}
rs1 = rs - (ez->max_t + 1);
qs1 = qs - (ez->max_q + 1);
mm_seq_rev(qs - qs0, qseq);
@ -185,8 +187,10 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, 0, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
}
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
int j;
for (j = i - 1; j >= 0; --j)
@ -197,7 +201,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qe1 = qe + (ez->max_q + 1);
mm_reg_split(r, r2, j + 1, qlen, a);
break;
} else {
} else { // FIXME: in rare cases, r->p can be NULL, which leads to a segfault
r->p->score += ez->score;
}
rs = re, qs = qe;
@ -208,9 +212,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qe];
mm_idx_getseq(mi, rid, re, re0, tseq);
ksw_extz2_sse(km, qe0 - qe, qseq, re0 - re, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
r->p->score += ez->max;
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
r->p->score += ez->max;
}
re1 = re + (ez->max_t + 1);
qe1 = qe + (ez->max_q + 1);
} else if (r2->cnt == 0) {

2
chain.c
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@ -40,7 +40,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *
for (j = i - 1; j >= st; --j) {
int64_t dr = ri - a[j].x;
int32_t dq = qi - (int32_t)a[j].y, dd, sc;
if (dq <= 0 || dq > max_dist) continue;
if (dr == 0 || dq <= 0 || dq > max_dist) continue;
if (t[j] == i) {
if (p[j] >= 0) t[p[j]] = i;
if (++n_skip > max_skip) break;

1
index.c
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@ -371,6 +371,7 @@ mm_idx_t *mm_idx_load(FILE *fp)
fread(s->name, 1, l, fp);
s->name[l] = 0;
fread(&s->len, 4, 1, fp);
s->offset = sum_len;
sum_len += s->len;
}
for (i = 0; i < 1<<mi->b; ++i) {

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r76-pre"
#define MM_VERSION "2.0-r77-pre"
void liftrlimit()
{

2
map.c
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@ -55,7 +55,7 @@ mm_tbuf_t *mm_tbuf_init(void)
{
mm_tbuf_t *b;
b = (mm_tbuf_t*)calloc(1, sizeof(mm_tbuf_t));
b->km = km_init();
// b->km = km_init();
b->sdb = sdust_buf_init(b->km);
return b;
}