X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=de556796b15685ede8723e928f0d8838a9098ada;hp=946ba7b4e98d584081b846105bde5f438f6e3ba1;hb=e42445c748ed193f8d0a4277a844fa848f30c132;hpb=fa217aa47313e2535cbd2d4bb034cfd405162662

diff --git a/NEWS b/NEWS
index 946ba7b..de55679 100644
--- a/NEWS
+++ b/NEWS
@@ -1,4 +1,37 @@
-Beta release 0.1.14 (16 March, 2011)
+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
@@ -9,17 +42,41 @@ 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.
+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.
 
-Other new features:
+ * 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.
 
- * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
-   older which encode PL in a different way.
+ * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
 
-(0.1.14: 16 March 2011, r930:163)
+(0.1.14: 21 March 2011, r933:170)