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r365: bugfix - wrong alignment (right mapping) 

The bug only happens when there is a 1bp del and 1bp ins which are close to the
end and there are no other substitutions or indels. In this case, bwa mem gave
a wrong band width.
This commit is contained in:
Heng Li 2013-03-15 11:59:05 -04:00
parent e5355fe3a0
commit dd51177837
2 changed files with 4 additions and 4 deletions
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6
bwamem.c
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@ -556,7 +556,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
int prev = a->score;
aw[0] = opt->w << i;
a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
if (bwa_verbose >= 4) printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout);
if (bwa_verbose >= 4) { printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); }
if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break;
}
// check whether we prefer to reach the end of the query
@ -574,7 +574,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
int prev = a->score;
aw[1] = opt->w << i;
a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
if (bwa_verbose >= 4) printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout);
if (bwa_verbose >= 4) { printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); }
if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break;
}
// similar to the above
@ -601,7 +601,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
static inline int infer_bw(int l1, int l2, int score, int a, int q, int r)
{
int w;
if (l1 == l2 && l1 * a - score < (q + r)<<1) return 0; // to get equal alignment length, we need at least two gaps
if (l1 == l2 && l1 * a - score < (q + r - a)<<1) return 0; // to get equal alignment length, we need at least two gaps
w = ((double)((l1 < l2? l1 : l2) * a - score - q) / r + 1.);
if (w < abs(l1 - l2)) w = abs(l1 - l2);
return w;

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.2-r364-beta"
#define PACKAGE_VERSION "0.7.2-r365-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);