X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=8455b484a0ce46bac6ca004e8ef2e2fb6e8239cf;hp=6b4d8aac5ede779b7efee6e02969dea40926275c;hb=c34624801b980425af68c3c431423c72b18c14fe;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9

diff --git a/NEWS b/NEWS
index 6b4d8aa..8455b48 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,84 @@
+Beta release 0.1.13 (1 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The most important though largely invisible modification is the change of the
+order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
+spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
+generated by samtools older than r921 inclusive.  VCF/BCF generated by the new
+samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
+version number.
+
+Single Individual Haplotyping (SIH) is added as an experimental feature. It
+originally aims to produce haploid consensus from fosmid pool sequencing, but
+also works with short-read data. For short reads, phased blocks are usually too
+short to be useful in many applications, but they can help to rule out part of
+SNPs close to INDELs or between copies of CNVs.
+
+
+Other notable changes in samtools:
+
+ * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
+   calling. This reduces the power but improves specificity.
+
+ * Improved sorting order checking in indexing. Now indexing is the preferred way
+   to check if a BAM is sorted.
+
+ * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
+   to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
+   a little loss in specificity.
+
+ * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
+
+ * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
+
+ * Added `mpileup -S' to compute per-sample strand bias P-value.
+
+ * Added `mpileup -G' to exclude read groups in variant calling.
+
+ * Fixed segfault in indel calling related to unmapped and refskip reads.
+
+ * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
+   genotypes for longer short INDELs, typically over 10bp.
+
+ * Fixed a bug in tview on big-endian machines.
+
+ * Fixed a very rare memory issue in bam_md.c
+
+ * Fixed an out-of-boundary bug in mpileup when the read base is `N'.
+
+ * Fixed a compiling error when the knetfile library is not used. Fixed a
+   library compiling error due to the lack of bam_nt16_nt4_table[] table.
+   Suppress a compiling warning related to the latest zlib.
+
+
+Other notable changes in bcftools:
+
+ * Updated the BCF spec.
+
+ * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
+   of all samples being the samei (identical to the reference or all homozygous
+   variants). Option `view -f' has been dropped.
+
+ * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
+   similar to "samtools.pl pileup2fq".
+
+ * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
+   spec. Drop bcf-fix.pl.
+
+ * Output bcftools specific INFO and FORMAT in the VCF header.
+
+ * Added `view -s' to call variants from a subset of samples.
+
+ * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
+   custom fields are still unparsed and will be stored as a missing value.
+
+ * Fixed a minor bug in Fisher's exact test; the results are rarely changed.
+
+
+(0.1.13: 1 March 2011, r926:134)
+
+
+
 Beta release 0.1.12a (2 December, 2010)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -532,4 +613,4 @@ 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
\ No newline at end of file
+http://samtools.sourceforge.net