From 408fd5e0727b0970ce362bb072ad44aa746456cb Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 23 Dec 2014 15:29:18 -0500
Subject: [PATCH] Released bwa-0.7.11-r1034

---
 NEWS.md | 13 +++++++++++--
 bwa.1   |  5 ++---
 main.c  |  2 +-
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 4be1dfc..fd42fa3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-Release 0.7.11 (XX December, 2014)
+Release 0.7.11 (23 December, 2014)
 ----------------------------------
 
 A major change to BWA-MEM is the support of mapping to ALT contigs in addition
@@ -47,7 +47,16 @@ Other notable changes to BWA-MEM:
    writing SAM. This saves significant wall-clock time when reading from
    or writing to a slow Unix pipe.
 
-(0.7.11: XX December 2014, r10XX)
+With the new release, the recommended way to map Illumina reads to GRCh38 is to
+use the bwakit binary package:
+
+    bwa.kit/run-gen-ref hs38DH
+    bwa.kit/bwa index hs38DH.fa
+    bwa.kit/run-bwamem -t8 -H -o out-prefix hs38DH.fa read1.fq.gz read2.fq.gz | sh
+
+Please check bwa.kit/README.md for details and command line options.
+
+(0.7.11: 23 December 2014, r1034)
 
 
 
diff --git a/bwa.1 b/bwa.1
index 6e95c0b..9b681b7 100644
--- a/bwa.1
+++ b/bwa.1
@@ -1,4 +1,4 @@
-.TH bwa 1 "21 December 2014" "bwa-0.7.11-r1032" "Bioinformatics tools"
+.TH bwa 1 "23 December 2014" "bwa-0.7.11-r1034" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -614,6 +614,7 @@ R	0x0020	strand of the mate
 s	0x0100	the alignment is not primary
 f	0x0200	QC failure
 d	0x0400	optical or PCR duplicate
+S	0x0800	supplementary alignment
 .TE
 
 .PP
@@ -647,8 +648,6 @@ _
 XS	Suboptimal alignment score
 XF	Support from forward/reverse alignment
 XE	Number of supporting seeds
-_
-XP	Alt primary hits; format: /(chr,pos,CIGAR,mapQ,NM;)+/
 .TE
 
 .PP
diff --git a/main.c b/main.c
index 887ea28..e157df6 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r1027-dirty"
+#define PACKAGE_VERSION "0.7.11-r1034"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);