rpoplin 9d01670f62 Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3286 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-02 19:21:23 +00:00
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alignment	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
analyzecovariates	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +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 PG tag to bam header to let people know it's been cleaned.	2010-04-30 17:30:30 +00:00
oneoffprojects	Reorg of UG args; checking in first before upcoming changes that will break integration tests.	2010-04-30 14:48:46 +00:00
playground	Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations.	2010-05-02 19:21:23 +00:00
utils	Optimized the join(..) method.	2010-04-30 15:55:07 +00:00