+------------------------------------------------------------------------
+r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools.pl-0.1.1
+ * improve indelFilter to avoid filtering true indels. The new filter relies
+ on the new pileup indel line implemented in samtools-0.1.2-25
+
+------------------------------------------------------------------------
+r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.2-25
+ * change the pileup indel line to shows the number of alignments actually
+ containing indels
+
+------------------------------------------------------------------------
+r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+
+update ChangeLog from "svn log"
+
------------------------------------------------------------------------
r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
Changed paths:
+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+ * Fixed a bug in maq2sam: a tag name is obsolete.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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~