From 7664795ffb15a568b2e5e2dffe26f492f4f230e9 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Tue, 25 Oct 2011 13:00:41 -0400
Subject: [PATCH] fixed a minor issue about +/-1

---
 bntseq.h | 2 +-
 bwase.c  | 2 +-
 main.c   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bntseq.h b/bntseq.h
index 0becc01..843db64 100644
--- a/bntseq.h
+++ b/bntseq.h
@@ -79,7 +79,7 @@ extern "C" {
 
 static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
 {
-	return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - pos : pos;
+	return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
 }
 
 #endif
diff --git a/bwase.c b/bwase.c
index 124d6b4..76480d4 100644
--- a/bwase.c
+++ b/bwase.c
@@ -118,7 +118,7 @@ bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int l
 	/* NB: For gapped alignment, pacpos may not be correct, which will be fixed
 	 * in refine_gapped_core(). This line also determines the way "x" is
 	 * calculated in refine_gapped_core() when (ext < 0 && is_end == 0). */
-	if (is_rev) pos_f = pos_f < len? 0 : pos_f - len; // mapped to the forward strand
+	if (is_rev) pos_f = pos_f + 1 < len? 0 : pos_f - len + 1; // mapped to the forward strand
 	return pos_f; // FIXME: it is possible that pos_f < bns->anns[ref_id].offset
 }
 
diff --git a/main.c b/main.c
index eda54f4..bc4eca4 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.0-r63-dev"
+#define PACKAGE_VERSION "0.6.0-r64-dev"
 #endif
 
 static int usage()