zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
README-alt.md
View File

@ -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 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 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). 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 Nonetheless, postprocessing is recommended as it improves mapQ and gives more
@ -134,7 +136,7 @@ not to high resolution for now.
### Evaluating ALT Mapping ### Evaluating ALT Mapping
(To come later...) (Coming soon...)
## Problems and Future Development ## Problems and Future Development

9
bwamem.c
View File

@ -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); 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; kstring_t str;
kvec_t(mem_aln_t) aa; kvec_t(mem_aln_t) aa;
int k; int k, l;
char **XA = 0; char **XA = 0;
if (!(opt->flag & MEM_F_ALL)) if (!(opt->flag & MEM_F_ALL))
XA = mem_gen_alt(opt, bns, pac, a, s->l_seq, s->seq); XA = mem_gen_alt(opt, bns, pac, a, s->l_seq, s->seq);
kv_init(aa); kv_init(aa);
str.l = str.m = 0; str.s = 0; 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_alnreg_t *p = &a->a[k];
mem_aln_t *q; mem_aln_t *q;
if (p->score < opt->T) continue; 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->XA = XA? XA[k] : 0;
q->flag |= extra_flag; // flag secondary q->flag |= extra_flag; // flag secondary
if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score 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; 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 if (aa.n == 0) { // no alignments good enough; then write an unaligned record
mem_aln_t t; mem_aln_t t;

2
main.c
View File

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