chartl cf75caf653 java changes: ... VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object. DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change) scala changes: convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2) useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines) bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing) first draft of a private mutations pipeline which will be elaborated in future git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-12 05:10:45 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	java changes:	2010-12-12 05:10:45 +00:00
test	A TiTv-free approach for cutting variants! Apparently much better than previous approach, and will work for indels and SV will truly minor modifications to the code. Will discuss with methods group on Monday.	2010-12-11 23:08:13 +00:00