From: Heng Li <lh3@live.co.uk>
Date: Wed, 28 Jan 2009 13:31:12 +0000 (+0000)
Subject: Release SAMtools-0.1.2
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=6c4f7da62ca46d02f16284bf3e586fc9842413c5

Release SAMtools-0.1.2
---

diff --git a/ChangeLog b/ChangeLog
index 0735557..1d47eac 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,33 @@
+------------------------------------------------------------------------
+r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/misc/indel_filter.pl
+
+Script for filtering indel results
+
+------------------------------------------------------------------------
+r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/misc/zoom2sam.pl
+
+convert ZOOM to SAM
+
+------------------------------------------------------------------------
+r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/misc/novo2sam.pl
+
+add a script to convert novo alignment to SAM
+
+------------------------------------------------------------------------
+r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/ChangeLog.old
+   M /trunk/samtools/samtools.1
+
+update documentation and ChangeLog
+
 ------------------------------------------------------------------------
 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
 Changed paths:
diff --git a/NEWS b/NEWS
index 1ed90ab..b53b3c9 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,72 @@
+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)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/bamtk.c b/bamtk.c
index dd9aa26..e162f07 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.1-19"
+#define PACKAGE_VERSION "0.1.2"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/samtools.1 b/samtools.1
index f7984cc..1bf96e6 100644
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "23 January 2009" "samtools-0.1.2" "Bioinformatics tools"
+.TH samtools 1 "28 January 2009" "samtools-0.1.2" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -320,7 +320,7 @@ Reference sequence names and lengths are not acquired from the BAM/SAM header.
 .IP o 2
 CIGAR operations N and P may not be properly handled.
 .IP o 2
-There is a small known memory leak in the viewer.
+There is a small memory leak in the viewer.
 
 .SH AUTHOR
 .PP