kiran 8ff93f77e6 Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3595 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-18 21:51:40 +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	Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval.	2010-06-18 21:51:40 +00:00
oneoffprojects	Mendelian Violation Classifier now filters violations on the fly via command line arguments; and closes unterminated homozygous regions at the end of a chromosome (so we see arms falling off in the file, rather than in the log)	2010-06-18 19:32:24 +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	Add some missing methods to the pileup architecture.	2010-06-18 15:03:08 +00:00