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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes: * In tview, do not show a blank screen when no reads mapped to the corresponding region. * Implemented native HTTP support in the BGZF library. Samtools is now able to directly open a BAM file on HTTP. HTTP proxy is also supported via the "http_proxy" environmental variable. * Samtools is now compitable with the MinGW (win32) compiler and the PDCurses library. * The calmd (or fillmd) command now calculates the NM tag and replaces MD tags if they are wrong. * The view command now recognizes and optionally prints FLAG in HEXs or strings to make a SAM file more friendly to human eyes. This is a samtools-C extension, not implemented in Picard for the time being. Please type `samtools view -?' for more information. * BAM files now have an end-of-file (EOF) marker to facilitate truncation detection. A warning will be given if an on-disk BAM file does not have this marker. The warning will be seen on BAM files generated by an older version of samtools. It does NO harm. * New key bindings in tview: `r' to show read names and `s' to show reference skip (N operation) as deletions. * Fixed a bug in `samtools merge -n'. * Samtools merge now optionally copies the header of a user specified SAM file to the resultant BAM output. * Samtools pileup/tview works with a CIGAR with the first or the last operation is an indel. * Fixed a bug in bam_aux_get(). Changes in other utilies: * Fixed wrong FLAG in maq2sam. (0.1.6: 2 September 2009, r453) Beta Release 0.1.5 (7 July, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes: * Support opening a BAM alignment on FTP. Users can now use "tview" to view alignments at the NCBI ftp site. Please read manual for more information. * In library, propagate errors rather than exit or complain assertion failure. * Simplified the building system and fixed compiling errors caused by zlib<1.2.2.1. * Fixed an issue about lost header information when a SAM is imported with "view -t". * Implemented "samtool.pl varFilter" which filters both SNPs and short indels. This command replaces "indelFilter". * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from pileup output. * In pileup, cap mapping quality at 60. This helps filtering when different aligners are in use. * In pileup, allow to output variant sites only. * Made pileup generate correct calls in repetitive region. At the same time, I am considering to implement a simplified model in SOAPsnp, although this has not happened yet. * In view, added '-u' option to output BAM without compression. This option is preferred when the output is piped to other commands. * In view, added '-l' and '-r' to get the alignments for one library or read group. The "@RG" header lines are now partially parsed. * Do not include command line utilities to libbam.a. * Fixed memory leaks in pileup and bam_view1(). * Made faidx more tolerant to empty lines right before or after FASTA > lines. Changes in other utilities: * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign. This release involves several modifications to the key code base which may potentially introduce new bugs even though we have tried to minimize this by testing on several examples. Please let us know if you catch bugs. (0.1.5: 7 July 2009, r373) Beta Release 0.1.4 (21 May, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes: * Added the 'rmdupse' command: removing duplicates for SE reads. * Fixed a critical bug in the indel caller: clipped alignments are not processed correctly. * Fixed a bug in the tview: gapped alignment may be incorrectly displayed. * Unified the interface to BAM and SAM I/O. This is done by implementing a wrapper on top of the old APIs and therefore old APIs are still valid. The new I/O APIs also recognize the @SQ header lines. * Generate the MD tag. * Generate "=" bases. However, the indel caller will not work when "=" bases are present. * Enhanced support of color-read display (by Nils Homer). * Implemented the GNU building system. However, currently the building system does not generate libbam.a. We will improve this later. For the time being, `make -f Makefile.generic' is preferred. * Fixed a minor bug in pileup: the first read in a chromosome may be skipped. * Fixed bugs in bam_aux.c. These bugs do not affect other components as they were not used previously. * Output the 'SM' tag from maq2sam. (0.1.4: 21 May 2009, r297) Beta Release 0.1.3 (15 April, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in SAMtools: * SAMtools is more consistent with the specification: a) '*' in the QUAL field is allowed; b) the field separator is TAB only and SPACE is treated as a character in a field; c) empty header is allowed. * Implemented GLFv3 support in pileup. * Fixed a severe bug in fixmate: strand information is wrongly overwritten. * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are not correctly retrieved sometimes. * Fixed a bug in rmdup: segfault if unmapped reads are present. * Move indel_filter.pl to samtools.pl and improved the filtering by checking the actual number of alignments containing indels. The indel pileup line is also changed a little to make this filtration easier. * Fixed a minor bug in indexing: the bin number of an unmapped read is wrongly calculated. * Added `flagstat' command to show statistics on the FLAG field. * Improved indel caller by setting the maximum window size in local realignment. Changes in other utilities: * Fixed a bug in maq2sam: a tag name is obsolete. * Improvement to wgsim: a) added support for SOLiD read simulation; b) show the number of substitutions/indels/errors in read name; c) considerable code clean up. * Various converters: improved functionality in general. * Updated the example SAM due to the previous bug in fixmate. (0.1.3: 15 April 2009, r227) Beta Release 0.1.2 (28 January, 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in SAMtools: * Implemented a Bayesian indel caller. The new caller generate scores and genotype and is potentially more accurate than Maq's indel caller. The pileup format is also changed accordingly. * Implemented rmdup command: remove potential PCR duplicates. Note that this command ONLY works for FR orientation and requires ISIZE is correctly set. * Added fixmate command: fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment. * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved. * Allow to select reads shown in the pileup output with a mask. * Generate GLFv2 from pileup. * Added two more flags for flagging PCR/optical duplicates and for QC failure. * Fixed a bug in sort command: name sorting for large alignment did not work. * Allow to completely disable RAZF (using Makefile.lite) as some people have problem to compile it. * Fixed a bug in import command when there are reads without coordinates. * Fixed a bug in tview: clipping broke the alignment viewer. * Fixed a compiling error when _NO_CURSES is applied. * Fixed a bug in merge command. Changes in other utilities: * Added wgsim, a paired-end reads simulator. Wgsim was adapted from maq's reads simulator. Colin Hercus further improved it to allow longer indels. * Added wgsim_eval.pl, a script that evaluates the accuracy of alignment on reads generated by wgsim. * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not work properly when multiple hits are output. * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will be retained when multiple hits are present. * Fixed a bug in export2sam.pl for QC reads. * Support RG tag at MAQ->SAM converter. * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and indel are not properly handled, though. * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the default Illumina output. (0.1.2: 28 January 2008; r116) 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