From d59d78838cbf918f462dfc06d58064b7a828b287 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 30 Apr 2014 14:55:44 -0400
Subject: [PATCH] r737: fixed an assertion when failed to convert sa

A bug pointed out by Mikkle Schubert
---
 bwape.c | 1 +
 main.c  | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/bwape.c b/bwape.c
index 82fc50b..a5dc3ad 100644
--- a/bwape.c
+++ b/bwape.c
@@ -297,6 +297,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 				p[j]->seQ = p[j]->mapQ = bwa_approx_mapQ(p[j], max_diff);
 				p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len + p[j]->ref_shift, &strand);
 				p[j]->strand = strand;
+				if (p[j]->pos == (bwtint_t)-1) p[j]->type = BWA_TYPE_NO_MATCH;
 			}
 		}
 	}
diff --git a/main.c b/main.c
index 7394f5f..bcbcb22 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8-r736-dirty"
+#define PACKAGE_VERSION "0.7.8-r737-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);