X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=946ba7b4e98d584081b846105bde5f438f6e3ba1;hp=8e0ba351ba15c148491119e45b2c1531ded6f66c;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/NEWS b/NEWS
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--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,369 @@
+Beta release 0.1.14 (16 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.
+
+Other new features:
+
+ * 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.
+
+(0.1.14: 16 March 2011, r930:163)
+
+
+
+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 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
+   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)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is another bug fix release:
+
+ * Fixed a memory violation in mpileup, which causes segfault. Release
+   0.1.9 and above are affected.
+
+ * Fixed a memory violation in the indel caller, which does not causes
+   segfault, but may potentially affect deletion calls in an unexpected
+   way. Release 0.1.10 and above are affected.
+
+ * Fixed a bug in computing r-square in bcftools. Few are using this
+   functionality and it only has minor effect.
+
+ * Fixed a memory leak in bam_fetch().
+
+ * Fixed a bug in writing meta information to the BAM index for the last
+   sequence. This bug is invisible to most users, but it is a bug anyway.
+
+ * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
+
+(0.1.12: 2 December 2010, r862)
+
+
+
+Beta release 0.1.11 (21 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is mainly a bug fix release:
+
+ * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
+   are retrieved from a small region containing no reads.
+
+ * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
+   failure when the first CIGAR operation is a deletion.
+
+ * Improved fault tolerence in remote access.
+
+One minor feature has been implemented in bcftools:
+
+ * Added a reference-free variant calling mode. In this mode, a site is
+   regarded as a variat iff the sample(s) contains two or more alleles;
+   the meaning of the QUAL field in the VCF output is changed
+   accordingly. Effectively, the reference allele is irrelevant to the
+   result in the new mode, although the reference sequence has to be
+   used in realignment when SAMtools computes genotype likelihoods.
+
+In addition, since 0.1.10, the `pileup' command has been deprecated by
+`mpileup' which is more powerful and more accurate. The `pileup' command
+will not be removed in the next few releases, but new features will not
+be added.
+
+(0.1.11: 21 November 2010, r851)
+
+
+
+Beta Release 0.1.10 (16 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release is featured as the first major improvement to the indel
+caller. The method is similar to the old one implemented in the pileup
+command, but the details are handled more carefully both in theory and
+in practice. As a result, the new indel caller usually gives more
+accurate indel calls, though at the cost of sensitivity. The caller is
+implemented in the mpileup command and is invoked by default. It works
+with multiple samples.
+
+Other notable changes:
+
+ * With the -r option, the calmd command writes the difference between
+   the original base quality and the BAQ capped base quality at the BQ
+   tag but does not modify the base quality. Please use -Ar to overwrite
+   the original base quality (the 0.1.9 behavior).
+
+ * Allow to set a maximum per-sample read depth to reduce memory. In
+   0.1.9, most of memory is wasted for the ultra high read depth in some
+   regions (e.g. the chr1 centromere).
+
+ * Optionally write per-sample read depth and per-sample strand bias
+   P-value.
+
+ * Compute equal-tail (Bayesian) credible interval of site allele
+   frequency at the CI95 VCF annotation.
+
+ * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
+   filtering.
+
+(0.1.10: 16 November 2010, r829)
+
+
+
+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)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable functional changes:
+
+ * Added the `reheader' command which replaces a BAM header with a new
+   header. This command is much faster than replacing header by
+   BAM->SAM->BAM conversions.
+
+ * Added the `mpileup' command which computes the pileup of multiple
+   alignments.
+
+ * The `index' command now stores the number of mapped and unmapped
+   reads in the index file. This information can be retrieved quickly by
+   the new `idxstats' command.
+
+ * By default, pileup used the SOAPsnp model for SNP calling. This
+   avoids the floating overflow in the MAQ model which leads to spurious
+   calls in repetitive regions, although these calls will be immediately
+   filtered by varFilter.
+
+ * The `tview' command now correctly handles CIGARs like 7I10M and
+   10M1P1I10M which cause assertion failure in earlier versions.
+
+ * Tview accepts a region like `=10,000' where `=' stands for the
+   current sequence name. This saves typing for long sequence names.
+
+ * Added the `-d' option to `pileup' which avoids slow indel calling
+   in ultradeep regions by subsampling reads locally.
+
+ * Added the `-R' option to `view' which retrieves alignments in read
+   groups listed in the specified file.
+
+Performance improvements:
+
+ * The BAM->SAM conversion is up to twice faster, depending on the
+   characteristic of the input.
+
+ * Parsing SAM headers with a lot of reference sequences is now much
+   faster.
+
+ * The number of lseek() calls per query is reduced when the query
+   region contains no read alignments.
+
+Bug fixes:
+
+ * Fixed an issue in the indel caller that leads to miscall of indels.
+   Note that this solution may not work well when the sequencing indel
+   error rate is higher than the rate of SNPs.
+
+ * Fixed another issue in the indel caller which may lead to incorrect
+   genotype.
+
+ * Fixed a bug in `sort' when option `-o' is applied.
+
+ * Fixed a bug in `view -r'.
+
+APIs and other changes:
+
+ * Added iterator interfaces to random access and pileup. The callback
+   interfaces directly call the iterator interfaces.
+
+ * The BGZF blocks holding the BAM header are indepedent of alignment
+   BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
+   fully contained in one BGZF block. This change is fully compatible
+   with the old version of samtools/picard.
+
+Changes in other utilities:
+
+ * Updated export2sam.pl by Chris Saunders.
+
+ * Improved the sam2vcf.pl script.
+
+ * Added a Python version of varfilter.py by Aylwyn Scally.
+
+(0.1.8: 11 July 2010, r613)
+
+
+
+Beta Release 0.1.7 (10 November, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Improved the indel caller in complex scenariors, in particular for
+   long reads. The indel caller is now able to make reasonable indel
+   calls from Craig Venter capillary reads.
+
+ * Rewrote single-end duplicate removal with improved
+   performance. Paired-end reads are not touched.
+
+ * Duplicate removal is now library aware. Samtools remove potential
+   PCR/optical dupliates inside a library rather than across libraries.
+
+ * SAM header is now fully parsed, although this functionality is not
+   used in merging and so on.
+
+ * In samtools merge, optionally take the input file name as RG-ID and
+   attach the RG tag to each alignment.
+
+ * Added FTP support in the RAZF library. RAZF-compressed reference
+   sequence can be retrieved remotely.
+
+ * Improved network support for Win32.
+
+ * Samtools sort and merge are now stable.
+
+Changes in other utilities:
+
+ * Implemented sam2vcf.pl that converts the pileup format to the VCF
+   format.
+
+ * This release of samtools is known to work with the latest
+   Bio-Samtools Perl module.
+
+(0.1.7: 10 November 2009, r510)
+
+
+
 Beta Release 0.1.6 (2 September, 2009)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -272,4 +638,4 @@ 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