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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chartl	java changes:	2010-12-12 05:10:45 +00:00
depristo	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
examples	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
hanna	Trying out Queue for the first time.	2010-11-18 18:29:12 +00:00
kshakir	Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:	2010-12-10 04:36:06 +00:00
rpoplin	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
fullCallingPipeline.q	Removing old arguments. We'll now be running with the defaults.	2010-12-09 18:58:56 +00:00
recalibrate.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00