From 3d2450ed970b503c68bbbd43d0bc2984bde86676 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 23 May 2013 12:45:14 -0400
Subject: [PATCH] r395: bugfix - hard clipping not applied on revaln

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

diff --git a/bwamem.c b/bwamem.c
index bfc2811..c0bd0ab 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -714,8 +714,8 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
 	} else { // the reverse strand
 		int i, qb = 0, qe = s->l_seq;
 		if (p->n_cigar) {
-			if ((p->cigar[0]&0xf) == 4) qe -= p->cigar[0]>>4;
-			if ((p->cigar[p->n_cigar-1]&0xf) == 4) qb += p->cigar[p->n_cigar-1]>>4;
+			if (which && ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3)) qe -= p->cigar[0]>>4;
+			if (which && ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3)) qb += p->cigar[p->n_cigar-1]>>4;
 		}
 		ks_resize(str, str->l + (qe - qb) + 1);
 		for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];
diff --git a/main.c b/main.c
index 96dde70..72877e4 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.4-r394-beta"
+#define PACKAGE_VERSION "0.7.4-r395-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);