ebanks 824c2bbac0 Finishing previous checkin ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-22 17:21:38 +00:00
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alignment	BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.	2010-05-20 14:05:13 +00:00
analyzecovariates	Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.	2010-06-18 17:37:11 +00:00
commandline	Fixing command line parsing to accept negative number arguments. Command line definitions must now start with a letter or underscore; previously, they could start with a digit.	2010-06-21 21:54:31 +00:00
gatk	Removing Beagle output from UG. Use ProduceBeagleInput walker instead (since it can be run post-filtration and respects the FILTER column).	2010-06-22 16:56:37 +00:00
oneoffprojects	incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet.	2010-06-22 06:31:05 +00:00
playground	Finishing previous checkin	2010-06-22 17:21:38 +00:00
queue/util	Fix for a reflection issue with generic types.	2010-06-16 15:58:38 +00:00
utils	Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.	2010-06-21 21:49:41 +00:00