From 7c50bad56782b65dcad4b9fbf5867e8e9b3a8ccc Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 31 Jan 2014 12:58:21 -0500
Subject: [PATCH] Release bwa-0.7.6a-r433

---
 bwa.c  | 5 +++--
 main.c | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/bwa.c b/bwa.c
index 21b71b8..aec04d8 100644
--- a/bwa.c
+++ b/bwa.c
@@ -128,8 +128,9 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
 		int k, x, y, u, n_mm = 0, n_gap = 0;
 		str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR
 		for (k = 0, x = y = u = 0; k < *n_cigar; ++k) {
-			int op  = cigar[k]&0xf;
-			int len = cigar[k]>>4;
+			int op, len;
+			cigar = (uint32_t*)str.s;
+			op  = cigar[k]&0xf, len = cigar[k]>>4;
 			if (op == 0) { // match
 				for (i = 0; i < len; ++i) {
 					if (query[x + i] != rseq[y + i]) {
diff --git a/main.c b/main.c
index 0a22f69..f872917 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.6-r432"
+#define PACKAGE_VERSION "0.7.6a-r433"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);