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r1037: wrong read number flag

This commit is contained in:
Heng Li 2014-12-24 00:55:33 -05:00
parent b9bbf2d3df
commit 3ae8d4b80b
2 changed files with 3 additions and 3 deletions
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4
bwamem_pair.c
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@ -334,12 +334,12 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
for (i = 0; i < 2; ++i) {
h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[z[i]]);
h[i].mapq = q_se[i];
h[i].flag |= 0x40 | extra_flag;
h[i].flag |= 0x40<<i | extra_flag;
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 | extra_flag;
g[i].flag |= 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-r1036-dirty"
#define PACKAGE_VERSION "0.7.11-r1037-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);