+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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
projects / samtools.git / blobdiff