From ac32543c12eac42f12e0c66b78c3d53211caeaab Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 28 Oct 2010 02:47:47 +0000
Subject: [PATCH] Release samtools-0.1.9 (r783)

---
 ChangeLog  | 21 +++++++++++++++++++++
 NEWS       | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 bamtk.c    |  2 +-
 samtools.1 |  3 +++
 4 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/ChangeLog b/ChangeLog
index d46ea25..12908c9 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,24 @@
+------------------------------------------------------------------------
+r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+fixed a silly bug in pileup
+
+------------------------------------------------------------------------
+r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bam_sort.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+ * samtools-0.1.8-22 (r781)
+ * made BAQ the default behavior of mpileup
+ * updated manual
+ * in merge, force to exit given inconsistent header when "-R" is not in use.
+
 ------------------------------------------------------------------------
 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
 Changed paths:
diff --git a/NEWS b/NEWS
index 28d6aaa..82646ba 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,52 @@
+Beta Release 0.1.9 (27 October, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release is featured as the first major improvement to the samtools'
+SNP caller.  It comes with a revised MAQ error model, the support of
+multi-sample SNP calling and the computation of base alignment quality
+(BAQ).
+
+The revised MAQ error model is based on the original model. It solves an
+issue of miscalling SNPs in repetitive regions. Althought such SNPs can
+usually be filtered at a later step, they mess up unfiltered calls. This
+is a theoretical flaw in the original model. The revised MAQ model
+deprecates the orginal MAQ model and the simplified SOAPsnp model.
+
+Multi-sample SNP calling is separated in two steps. The first is done by
+samtools mpileup and the second by a new program, bcftools, which is
+included in the samtools source code tree. Multi-sample SNP calling also
+works for single sample and has the advantage of enabling more powerful
+filtration. It is likely to deprecate pileup in future once a proper
+indel calling method is implemented.
+
+BAQ is the Phred-scaled probability of a read base being wrongly
+aligned. Capping base quality by BAQ has been shown to be very effective
+in suppressing false SNPs caused by misalignments around indels or in
+low-complexity regions with acceptable compromise on computation
+time. This strategy is highly recommended and can be used with other SNP
+callers as well.
+
+In addition to the three major improvements, other notable changes are:
+
+ * Changes to the pileup format. A reference skip (the N CIGAR operator)
+   is shown as '<' or '>' depending on the strand. Tview is also changed
+   accordingly.
+
+ * Accelerated pileup. The plain pileup is about 50% faster.
+
+ * Regional merge. The merge command now accepts a new option to merge
+   files in a specified region.
+
+ * Fixed a bug in bgzip and razip which causes source files to be
+   deleted even if option -c is applied.
+
+ * In APIs, propogate errors to downstream callers and make samtools
+   return non-zero values once errors occur.
+
+(0.1.9: 27 October 2010, r783)
+
+
+
 Beta Release 0.1.8 (11 July, 2010)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/bamtk.c b/bamtk.c
index aabc5ae..082767c 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-22 (r781)"
+#define PACKAGE_VERSION "0.1.9 (r783)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/samtools.1 b/samtools.1
index 77b5a22..cc421d4 100644
--- a/samtools.1
+++ b/samtools.1
@@ -606,6 +606,9 @@ consider to apply
 .B -C50
 to
 .BR mpileup .
+SNP calling in this way also works for single sample and has the
+advantage of enabling more powerful filtering. The drawback is the lack
+of short indel calling, which may be implemented in future.
 
 .IP o 2
 Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
-- 
2.39.2