ebanks df1cadc4c9 Fix NullPointerException when priority list is left out ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3600 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 13:46:54 +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	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Fix NullPointerException when priority list is left out	2010-06-21 13:46:54 +00:00
oneoffprojects	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
playground	Add -noVerbose flag to stop output of INFO data.	2010-06-18 18:53:35 +00:00
queue/util	Fix for a reflection issue with generic types.	2010-06-16 15:58:38 +00:00
utils	Misc bug fixes: fix tracking of nInsertions with sample-split pileup constructor. Fix performance	2010-06-20 20:32:27 +00:00