Release BWA-0.7.3-r366

NEWS

@@ -1,3 +1,34 @@
+Release 0.7.3 (15 March, 2013)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Changes to BWA-MEM:
+
+ * Bugfix: pairing score is inaccurate when option -A does not take the default
+   value. This is a very minor issue even if it happens.
+
+ * Bugfix: occasionally wrong CIGAR. This happens when in the alignment there
+   is a 1bp deletion and a 1bp insertion which are close to the end of the
+   reads, and there are no other substitutions or indels. BWA-MEM would not do
+   a gapped alignment due to the bug.
+
+ * New feature: output other non-overlapping alignments in the XP tag such that
+   we can see the entire picture of alignment from one SAM line. XP gives the
+   position, CIGAR, NM and mapQ of each aligned subsequence of the query.
+
+BWA-MEM has been used to align ~300Gbp 100-700bp SE/PE reads. SNP/indel calling
+has also been evaluated on part of these data. BWA-MEM generally gives better
+pre-filtered SNP calls than BWA. No significant issues have been observed since
+0.7.2, though minor improvements or bugs (e.g. the bug fixed in this release)
+are still possible. If you find potential issues, please send bug reports to
+<bio-bwa-help@lists.sourceforge.net> (free registration required).
+
+In addition, more detailed description of the BWA-MEM algorithm can be found at
+<https://github.com/lh3/mem-paper>.
+
+(0.7.3: 15 March 2013, r366)
+
+
+
 Release 0.7.2 (9 March, 2013)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "13 March 2013" "bwa-0.7.3" "Bioinformatics tools"
+.TH bwa 1 "15 March 2013" "bwa-0.7.3" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -580,7 +580,7 @@ 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;)+/
+XP	Alt primary hits; format: /(chr,pos,CIGAR,mapQ,NM;)+/
 .TE
 
 .PP

main.c

@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.2-r365-beta"
+#define PACKAGE_VERSION "0.7.3-r366"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);