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r868: use soft clip for ALT hits

This commit is contained in:
Heng Li 2014-09-19 16:58:18 -04:00
parent 9af36064e8
commit 7426a750ec
2 changed files with 2 additions and 2 deletions
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2
bwamem.c
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@ -830,7 +830,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
if (p->n_cigar) { // aligned
for (i = 0; i < p->n_cigar; ++i) {
int c = p->cigar[i]&0xf;
if (!(opt->flag&MEM_F_SOFTCLIP) && (c == 3 || c == 4))
if (!(opt->flag&MEM_F_SOFTCLIP) && !p->is_alt && (c == 3 || c == 4))
c = which? 4 : 3; // use hard clipping for supplementary alignments
kputw(p->cigar[i]>>4, str); kputc("MIDSH"[c], str);
}

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r867-dirty"
#define PACKAGE_VERSION "0.7.10-r868-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);