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r1038: wrong 0x100|0x800 flags in PE mode

This commit is contained in:
Heng Li 2014-12-24 13:22:46 -05:00
parent 3ae8d4b80b
commit e746a3eac7
2 changed files with 5 additions and 3 deletions
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6
bwamem_pair.c
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@ -338,8 +338,10 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
h[i].XA = XA[i]? XA[i][z[i]] : 0;
aa[i][n_aa[i]++] = h[i];
if (n_pri[i] < a[i].n) { // the read has ALT hits
g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[n_pri[i]]);
g[i].flag |= 0x40<<i | extra_flag;
mem_alnreg_t *p = &a[i].a[n_pri[i]];
if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) continue;
g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, p);
g[i].flag |= 0x800 | 0x40<<i | extra_flag;
g[i].XA = XA[i]? XA[i][n_pri[i]] : 0;
aa[i][n_aa[i]++] = g[i];
}

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.11-r1037-dirty"
#define PACKAGE_VERSION "0.7.11-r1038-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);