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 Changes in other utilities: * Fixed a bug in maq2sam: a tag name is obsolete.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