From 11437a14f4050e9ede5b11d2719a45083d6648f4 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 23 Feb 2016 11:07:27 -0500
Subject: [PATCH] Port #48 to the dev branch

---
 NEWS.md | 29 +++++++++++++++++++++++++++++
 bwape.c |  2 +-
 bwase.c |  1 +
 3 files changed, 31 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 4692889e..d09544e7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,32 @@
+Release 0.7.13 (23 Feburary 2016)
+---------------------------------
+
+This release fixes a few minor bugs in the previous version and adds a few
+minor features. All BWA algorithms should produce identical output to 0.7.12
+when there are no ALT contigs.
+
+Detailed changes:
+
+ * Fixed a bug in "bwa-postalt.js". The old version may produce 0.5% of wrong
+   bases for reads mapped to the ALT contigs.
+
+ * Fixed a potential bug in the multithreading mode. It may occur when mapping
+   is much faster than file reading, which should almost never happen in
+   practice.
+
+ * Changed the download URL of GRCh38.
+
+ * Removed the read overlap mode. It is not working well.
+
+ * Added the ropebwt2 algorithm as an alternative to index large genomes.
+   Ropebwt2 is slower than the "bwtsw" algorithm, but it has a permissive
+   license. This allows us to create an Apache2-licensed BWA (in the "Apache2"
+   branch) for commercial users who are concerned with GPL.
+
+(0.7.13: 23 Feburary 2016, r1118)
+
+
+
 Release 0.7.12 (28 December 2014)
 ---------------------------------
 
diff --git a/bwape.c b/bwape.c
index a5dc3ad4..f2d3d8e0 100644
--- a/bwape.c
+++ b/bwape.c
@@ -379,7 +379,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 						bwt_multi1_t *q = p[j]->multi + k;
 						q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
 						q->strand = strand;
-						if (q->pos != p[j]->pos)
+						if (q->pos != p[j]->pos && q->pos != (bwtint_t)-1)
 							p[j]->multi[n_multi++] = *q;
 					}
 					p[j]->n_multi = n_multi;
diff --git a/bwase.c b/bwase.c
index cb912ec5..64808ef5 100644
--- a/bwase.c
+++ b/bwase.c
@@ -113,6 +113,7 @@ bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int r
 {
 	bwtint_t pos_f;
 	int is_rev;
+	*strand = 0;
 	pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate
 	if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1;
 	pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base