Beta Release 0.1.2 (28 January, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in SAMtools:

 * Implemented a Bayesian indel caller. The new caller generate scores
   and genotype and is potentially more accurate than Maq's indel
   caller. The pileup format is also changed accordingly.

 * Implemented rmdup command: remove potential PCR duplicates. Note that
   this command ONLY works for FR orientation and requires ISIZE is
   correctly set.

 * Added fixmate command: fill in mate coordinates, ISIZE and mate
   related flags from a name-sorted alignment.

 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.

 * Allow to select reads shown in the pileup output with a mask.

 * Generate GLFv2 from pileup.

 * Added two more flags for flagging PCR/optical duplicates and for QC
   failure.

 * Fixed a bug in sort command: name sorting for large alignment did not
   work.

 * Allow to completely disable RAZF (using Makefile.lite) as some people
   have problem to compile it.

 * Fixed a bug in import command when there are reads without
   coordinates.

 * Fixed a bug in tview: clipping broke the alignment viewer.

 * Fixed a compiling error when _NO_CURSES is applied.

 * Fixed a bug in merge command.

Changes in other utilities:

 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
   maq's reads simulator. Colin Hercus further improved it to allow
   longer indels.

 * Added wgsim_eval.pl, a script that evaluates the accuracy of
   alignment on reads generated by wgsim.

 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
   work properly when multiple hits are output.

 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
   be retained when multiple hits are present.

 * Fixed a bug in export2sam.pl for QC reads.

 * Support RG tag at MAQ->SAM converter.

 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
   indel are not properly handled, though.

 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
   default Illumina output.

(0.1.2: 28 January 2008; r116)



Beta Release 0.1.1 (22 December, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The is the first public release of samtools. For more information,
please check the manual page `samtools.1' and the samtools website
http://samtools.sourceforge.net