X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=b8b8bc74def5e030795f642c38340a07d664b82e;hb=bea524c4fd680119bdc118ec07ebe89722e2e697;hp=b53b3c9b48dd546b872085672dd3dcbab1f93664;hpb=ececa9f899791ea15517092f0bacffa98ca6512c;p=samtools.git

diff --git a/NEWS b/NEWS
index b53b3c9..b8b8bc7 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,46 @@
+Beta Release 0.1.3 (XX April, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in SAMtools:
+
+ * SAMtools is more consistent with the specification: a) '*' in the
+   QUAL field is allowed; b) the field separator is TAB only and SPACE
+   is treated as a character in a field; c) empty header is allowed.
+
+ * Implemented GLFv3 support in pileup.
+
+ * Fixed a severe bug in fixmate: strand information is wrongly
+   overwritten.
+
+ * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
+   not correctly retrieved sometimes.
+
+ * Move indel_filter.pl to samtools.pl and improved the filtering by
+   checking the actual number of alignments containing indels. The indel
+   pileup line is also changed a little to make this filtration easier.
+
+ * Fixed a minor bug in indexing: the bin number of an unmapped read is
+   wrongly calculated.
+
+ * Added `flagstat' command to show statistics on the FLAG field.
+
+ * Improved indel caller by setting the maximum window size in local
+   realignment.
+
+Changes in other utilities:
+
+ * Fixed a bug in maq2sam: a tag name is obsolete.
+
+ * Improvement to wgsim: a) added support for SOLiD read simulation; b)
+   show the number of substitutions/indels/errors in read name; c)
+   considerable code clean up.
+
+ * Various converters: improved functionality in general.
+
+(0.1.3: XX April 2009, rXXX)
+
+
+
 Beta Release 0.1.2 (28 January, 2008)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~