From 7426a750ec2ed9247d3bd597d9fec34169dea17d Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 19 Sep 2014 16:58:18 -0400
Subject: [PATCH] r868: use soft clip for ALT hits

---
 bwamem.c | 2 +-
 main.c   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index fcd0f26..394aa40 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -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);
 			}
diff --git a/main.c b/main.c
index 367d9d4..7a398f4 100644
--- a/main.c
+++ b/main.c
@@ -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[]);