X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=6b4d8aac5ede779b7efee6e02969dea40926275c;hp=8e0ba351ba15c148491119e45b2c1531ded6f66c;hb=cdd6f3c76a88cf064bffafc460b358557bc603b3;hpb=d363084f0412f3bcdeb0304aeb0974c9a10c7649 diff --git a/NEWS b/NEWS index 8e0ba35..6b4d8aa 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,263 @@ +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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~