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:

 * 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.

 * 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.

 * 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 * Fixed a bug in maq2sam: a tag name is obsolete.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.

 * Updated the example SAM due to the previous bug in fixmate.

(0.1.3: 15 April 2009, r227)



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