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r78: fixed a split bug

This commit is contained in:
Heng Li 2017-06-26 14:45:23 -04:00
parent de54c9dac2
commit 5b614ae828
3 changed files with 6 additions and 5 deletions
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8
align.c
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@ -179,10 +179,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qs1 = qs - (ez->max_q + 1);
mm_seq_rev(qs - qs0, qseq);
} else rs1 = rs, qs1 = qs;
re1 = rs, qe1 = qs;
assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < r->cnt; ++i) { // gap filling
mm_adjust_minier(mi, qseq0, &a[r->as + i], &re, &qe);
re1 = re, qe1 = qe;
if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
@ -197,8 +199,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if ((int32_t)a[r->as + j].x < re + ez->max_t)
break;
r->p->score += ez->max;
re1 = re + (ez->max_t + 1);
qe1 = qe + (ez->max_q + 1);
re1 = rs + (ez->max_t + 1);
qe1 = qs + (ez->max_q + 1);
mm_reg_split(r, r2, j + 1, qlen, a);
break;
} else { // FIXME: in rare cases, r->p can be NULL, which leads to a segfault
@ -219,8 +221,6 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
}
re1 = re + (ez->max_t + 1);
qe1 = qe + (ez->max_q + 1);
} else if (r2->cnt == 0) {
re1 = re, qe1 = qe;
}
assert(qe1 <= qlen);

2
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r77-pre"
#define MM_VERSION "2.0-r78-pre"
void liftrlimit()
{

1
map.c
View File

@ -302,6 +302,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
mm_reg1_t *regs;
if (mm_verbose >= 10) fprintf(stderr, "===> %s <===\n", qname);
b->mini.n = 0;
mm_sketch(b->km, seq, l_seq, mi->w, mi->k, 0, mi->is_hpc, &b->mini);
if (opt->sdust_thres > 0)