-Beta Release 0.1.3 (XX April, 2009)
+Beta Release 0.1.4 (21 May, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Added the 'rmdupse' command: removing duplicates for SE reads.
+
+ * Fixed a critical bug in the indel caller: clipped alignments are not
+ processed correctly.
+
+ * Fixed a bug in the tview: gapped alignment may be incorrectly
+ displayed.
+
+ * Unified the interface to BAM and SAM I/O. This is done by
+ implementing a wrapper on top of the old APIs and therefore old APIs
+ are still valid. The new I/O APIs also recognize the @SQ header
+ lines.
+
+ * Generate the MD tag.
+
+ * Generate "=" bases. However, the indel caller will not work when "="
+ bases are present.
+
+ * Enhanced support of color-read display (by Nils Homer).
+
+ * Implemented the GNU building system. However, currently the building
+ system does not generate libbam.a. We will improve this later. For
+ the time being, `make -f Makefile.generic' is preferred.
+
+ * Fixed a minor bug in pileup: the first read in a chromosome may be
+ skipped.
+
+ * Fixed bugs in bam_aux.c. These bugs do not affect other components as
+ they were not used previously.
+
+ * Output the 'SM' tag from maq2sam.
+
+(0.1.4: 21 May 2009, r297)
+
+
+
+Beta Release 0.1.3 (15 April, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Notable changes in SAMtools:
* Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
not correctly retrieved sometimes.
+ * Fixed a bug in rmdup: segfault if unmapped reads are present.
+
* 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.
* Various converters: improved functionality in general.
-(0.1.3: XX April 2009, rXXX)
+ * Updated the example SAM due to the previous bug in fixmate.
+
+(0.1.3: 15 April 2009, r227)