From 1c19bc630f7cade6a27914f687bc4c862b3e567f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 25 Feb 2014 01:05:37 -0500
Subject: [PATCH] Released bwa-0.7.7-r441

---
 NEWS   | 17 +++++++++++++++++
 bwa.1  |  2 +-
 main.c |  2 +-
 3 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/NEWS b/NEWS
index eb9c37a..a7c64ed 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,20 @@
+Release 0.7.7 (25 Feburary, 2014)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release fixes incorrect MD tags in the BWA-MEM output.
+
+A note about short-read mapping to GRCh38. The new human reference genome
+GRCh38 contains 60Mbp program generated alpha repeat arrays, some of which are
+hard masked as they cannot be localized. These highly repetitive arrays make
+BWA-MEM ~50% slower. If you are concerned with the performance of BWA-MEM, you
+may consider to use option "-c2000 -m50". On simulated data, this setting helps
+the performance at a very minor cost on accuracy. I may consider to change the
+default in future releases.
+
+(0.7.7: 25 Feburary 2014, r441)
+
+
+
 Release 0.7.6 (31 Januaray, 2014)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/bwa.1 b/bwa.1
index 5949a1b..601a529 100644
--- a/bwa.1
+++ b/bwa.1
@@ -1,4 +1,4 @@
-.TH bwa 1 "31 January 2014" "bwa-0.7.6" "Bioinformatics tools"
+.TH bwa 1 "25 Feburary 2014" "bwa-0.7.7" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
diff --git a/main.c b/main.c
index 803cf10..a8df9c0 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.6a+dev-r440"
+#define PACKAGE_VERSION "0.7.7-r441"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);