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r370: suppress "D" at the end of a cigar 

This is caused by seeds in tandem repeats, in which case, bwa-mem may not
extend the true seed. The change in this commit is only a temporary cure.
This commit is contained in:
Heng Li 2013-04-03 23:57:19 -04:00
parent 8437cd4edd
commit 1e118e0823
2 changed files with 8 additions and 1 deletions
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7
bwamem.c
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@ -863,6 +863,13 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
a.NM = NM;
pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
a.is_rev = is_rev;
if (a.n_cigar > 0) {
if ((a.cigar[0]&0xf) == 2) {
pos += a.cigar[0]>>4;
--a.n_cigar;
memmove(a.cigar, a.cigar + 1, a.n_cigar * 4);
} else if ((a.cigar[a.n_cigar-1]&0xf) == 2) --a.n_cigar;
}
if (qb != 0 || qe != l_query) { // add clipping to CIGAR
int clip5, clip3;
clip5 = is_rev? l_query - qe : qb;

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r369-beta"
#define PACKAGE_VERSION "0.7.3-r370-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);