From ebb7b02e9b5346c05c8bed12f016df812cc88455 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 9 Sep 2013 16:57:55 -0400
Subject: [PATCH] r414: fixed a bug caused by the last commit

---
 bwamem.c | 12 ++++++++++--
 main.c   |  2 +-
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index ebc2ac2..6cc4639 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -389,11 +389,19 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
 			mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
 			mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
 			if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
-				if (q->score < p->score) q->qe = q->qb;
-				else p->qe = p->qb;
+				if (p->score < q->score) {
+					p->qe = p->qb;
+					break;
+				} else q->qe = q->qb;
 			}
 		}
 	}
+	for (i = 0, m = 0; i < n; ++i) // exclude identical hits
+		if (a[i].qe > a[i].qb) {
+			if (m != i) a[m++] = a[i];
+			else ++m;
+		}
+	n = m;
 	ks_introsort(mem_ars, n, a);
 	for (i = 1; i < n; ++i) { // mark identical hits
 		if (a[i].score == a[i-1].score && a[i].rb == a[i-1].rb && a[i].qb == a[i-1].qb)
diff --git a/main.c b/main.c
index d5b61a7..d1e3895 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5a-r413"
+#define PACKAGE_VERSION "0.7.5a-r414"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);