X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=1956b6c33477f67be830554da520a7aa13a738ed;hb=e2a3ec4a7acf3ea9ac13e88bf4badd50132c81ce;hp=1ed90ab0d6f19f0bcfb044876a04e26d8efa1940;hpb=f93dae0d03856955f9424e8b2aaf261304ca647e;p=samtools.git

diff --git a/NEWS b/NEWS
index 1ed90ab..1956b6c 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,115 @@
+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.
+
+ * 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+ * Fixed a bug in maq2sam: a tag name is obsolete.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: 15 April 2009, rXXX)
+
+
+
+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)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~