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r940: fixed a bug - missing primary hit

This commit is contained in:
Heng Li 2014-10-21 12:57:49 -04:00
parent 5e00d08346
commit 282130a64e
3 changed files with 10 additions and 7 deletions
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6
README-alt.md
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@ -88,7 +88,9 @@ alignments and assigns mapQ following these two rules:
In theory, non-ALT alignments from step 1 should be identical to alignments
against a reference genome with ALT contigs. In practice, the two types of
alignments may differ in rare cases due to seeding heuristics.
alignments may differ in rare cases due to seeding heuristics. When an ALT hit
is significantly better than non-ALT hits, BWA-MEM may miss seeds on the
non-ALT hits. This happens more often for contig mapping.
If we don't care about ALT hits, we may skip postprocessing (step 2).
Nonetheless, postprocessing is recommended as it improves mapQ and gives more
@ -134,7 +136,7 @@ not to high resolution for now.
### Evaluating ALT Mapping
(To come later...)
(Coming soon...)
## Problems and Future Development

9
bwamem.c
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@ -980,14 +980,14 @@ void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, mem_alnreg_v *a, int l_query, const char *query);
kstring_t str;
kvec_t(mem_aln_t) aa;
int k;
int k, l;
char **XA = 0;
if (!(opt->flag & MEM_F_ALL))
XA = mem_gen_alt(opt, bns, pac, a, s->l_seq, s->seq);
kv_init(aa);
str.l = str.m = 0; str.s = 0;
for (k = 0; k < a->n; ++k) {
for (k = l = 0; k < a->n; ++k) {
mem_alnreg_t *p = &a->a[k];
mem_aln_t *q;
if (p->score < opt->T) continue;
@ -999,9 +999,10 @@ void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
q->XA = XA? XA[k] : 0;
q->flag |= extra_flag; // flag secondary
if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
if (k && p->secondary < 0) // if supplementary
if (l && p->secondary < 0) // if supplementary
q->flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
if (k && !p->is_alt && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
if (l && !p->is_alt && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
++l;
}
if (aa.n == 0) { // no alignments good enough; then write an unaligned record
mem_aln_t t;

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r939-dirty"
#define PACKAGE_VERSION "0.7.10-r940-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);