Release SAMtools-0.1.2

[samtools.git] / NEWS

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+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)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~