ebanks f0fc34bb8e Bug fix: N's are allowed in the ref so don't fail when e.g. dbsnp has an N! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3620 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-23 17:49:14 +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	Bug fix: N's are allowed in the ref so don't fail when e.g. dbsnp has an N!	2010-06-23 17:49:14 +00:00
oneoffprojects	Committing changes to comp overlap for indels. Passes all integration tests; minor changes to MVC walker.	2010-06-23 15:49:13 +00:00
playground	Finishing previous checkin	2010-06-22 17:21:38 +00:00
queue/util	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
utils	Rev Picard with performance enhancements.	2010-06-22 22:54:23 +00:00