X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=28d6aaa81269b72f0b8cb26a971c5bd55e33c050;hp=8e0ba351ba15c148491119e45b2c1531ded6f66c;hb=049705238f6c2d4cdd79022e7bcf2cc7d83ba9c7;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a diff --git a/NEWS b/NEWS index 8e0ba35..28d6aaa 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,122 @@ +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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~