Released bwa-0.7.11-r1034

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)
 
 
 

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

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[]);