ebanks 427a2f85e9 The Indel Realigner now lets the engine do all of the setup for args affecting the SAM writer. Thanks, Matt! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4141 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-27 15:19:47 +00:00
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alignment	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
analyzecovariates	Committing Michael Yourshaw's patch for AnalyzeCovariates. We spawn each RScript process and wait for it to finish in series. Thanks Michael!	2010-08-24 13:06:25 +00:00
commandline	The tagger was automatically combining identical tags, but this is a problem	2010-08-25 22:01:32 +00:00
gatk	The Indel Realigner now lets the engine do all of the setup for args affecting the SAM writer. Thanks, Matt!	2010-08-27 15:19:47 +00:00
oneoffprojects	Small fixes for consistency in the numbers.	2010-08-24 20:48:25 +00:00
playground	Cleaning up playground utils and tests	2010-08-27 01:25:47 +00:00
queue	Updated Queue GATK generation to reflect -B and -I changes.	2010-08-25 22:17:36 +00:00
utils	Small refactoring: make Haplotype a public class since it will be soon extended and shared with other callers.	2010-08-24 17:52:36 +00:00