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r960: XA tags occasionally missing for PE

This commit is contained in:
Heng Li 2014-10-28 13:43:26 -04:00
parent 6f39715e6e
commit 9867634f72
2 changed files with 8 additions and 8 deletions
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14
bwamem_pair.c
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@ -327,13 +327,13 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
// suboptimal hits // suboptimal hits
if (!(opt->flag & MEM_F_ALL)) { if (!(opt->flag & MEM_F_ALL)) {
for (i = 0; i < 2; ++i) { for (i = 0; i < 2; ++i) {
int k = a[i].a[z[i]].secondary; int k = a[i].a[z[i]].secondary_all;
if (k >= 0) { // switch secondary and primary if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
assert(a[i].a[k].secondary < 0); assert(a[i].a[k].secondary_all < 0);
for (j = 0; j < n_pri[i]; ++j) for (j = 0; j < a[i].n; ++j)
if (a[i].a[j].secondary == k || j == k) if (a[i].a[j].secondary_all == k || j == k)
a[i].a[j].secondary = z[i]; a[i].a[j].secondary_all = z[i];
a[i].a[z[i]].secondary = -1; a[i].a[z[i]].secondary_all = -1;
} }
XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq); XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq);
} }

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-r943-dirty" #define PACKAGE_VERSION "0.7.10-r960-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);