X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=a600bb1d2519fb4a139a406f223da55dddcc1b80;hp=8455b484a0ce46bac6ca004e8ef2e2fb6e8239cf;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=c34624801b980425af68c3c431423c72b18c14fe

diff --git a/NEWS b/NEWS
index 8455b48..a600bb1 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,122 @@
+Beta Release 0.1.16 (21 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in samtools:
+
+ * Support the new SAM/BAM type `B' in the latest SAM spec v1.4.
+
+ * When the output file of `samtools merge' exists, do not overwrite it unless
+   a new command-line option `-f' is applied.
+
+ * Bugfix: BED support is not working when the input BED is not sorted.
+
+ * Bugfix: some reads without coordinates but given on the reverse strand are
+   lost in merging.
+
+Notable changes in bcftools:
+
+ * Code cleanup: separated max-likelihood inference and Bayesian inference.
+
+ * Test Hardy-Weinberg equilibrium with a likelihood-ratio test.
+
+ * Provided another association test P-value by likelihood-ratio test.
+
+ * Use Brent's method to estimate the site allele frequency when EM converges
+   slowly. The resulting ML estimate of allele frequnecy is more accurate.
+
+ * Added the `ldpair' command, which computes r^2 between SNP pairs given in
+   an input file.
+
+Also, the `pileup' command, which has been deprecated by `mpileup' since
+version 0.1.10, will be dropped in the next release. The old `pileup' command
+is substandard and causing a lot of confusion.
+
+(0.1.16: 21 April 2011, r963:234)
+
+
+
+Beta Release 0.1.15 (10 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Noteable changes:
+
+ * Allow to perform variant calling or to extract information in multiple
+   regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
+   and `bcftools view -l').
+
+ * Added the `depth' command to samtools to compute the per-base depth with a
+   simpler interface. File `bam2depth.c', which implements this command, is the
+   recommended example on how to use the mpileup APIs.
+
+ * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
+   test using this estimate.
+
+ * For `samtools view', when `-R' is specified, drop read groups in the header
+   that are not contained in the specified file.
+
+ * For `samtools flagstat', separate QC-pass and QC-fail reads.
+
+ * Improved the command line help of `samtools mpileup' and `bcftools view'.
+
+ * Use a global variable to control the verbose level of samtools stderr
+   output. Nonetheless, it has not been full utilized.
+
+ * Fixed an issue in association test which may report false associations,
+   possibly due to floating point underflow.
+
+(0.1.15: 10 April 2011, r949:203)
+
+
+
+Beta release 0.1.14 (21 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release implements a method for testing associations for case-control
+data. The method does not call genotypes but instead sums over all genotype
+configurations to compute a chi^2 based test statistics. It can be potentially
+applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
+has not been evaluated on real data.
+
+Another new feature is to make X chromosome variant calls when female and male
+samples are both present. The user needs to provide a file indicating the
+ploidy of each sample (see also manual bcftools/bcftools.1).
+
+Other notable changes:
+
+ * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
+   older which encodes PL in a different way.
+
+ * Changed the behavior of `bcftools view -s'. Now when a list of samples is
+   provided, the samples in the output will be reordered to match the ordering
+   in the sample list. This change is mainly designed for association test.
+
+ * Sped up `bcftools view -v' for target sequencing given thousands of samples.
+   Also added a new option `view -d' to skip loci where only a few samples are
+   covered by reads.
+
+ * Dropped HWE test. This feature has never been implemented properly. An EM
+   should be much better. To be implemented in future.
+
+ * Added the `cat' command to samtools. This command concatenate BAMs with
+   identical sequence dictionaries in an efficient way. Modified from bam_cat.c
+   written by Chris Saunders.
+
+ * Added `samtools view -1' to write BAMs at a low compression level but twice
+   faster to create. The `sort' command generates temporary files at a low
+   compression level as well.
+
+ * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
+   strings (strictly speaking, such a file is not BAM).
+
+ * Added `samtools mpileup -L' to skip INDEL calling in regions with
+   excessively high coverage. Such regions dramatically slow down mpileup.
+
+ * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
+
+(0.1.14: 21 March 2011, r933:170)
+
+
+
 Beta release 0.1.13 (1 March, 2011)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -56,7 +175,7 @@ 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
+   of all samples being the same (identical to the reference or all homozygous
    variants). Option `view -f' has been dropped.
 
  * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence