aaron 28a1020c89 comment out debugging line that was clogging the performance test output. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4487 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-13 03:26:55 +00:00
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alignment	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
analyzecovariates	All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException.	2010-09-10 15:25:30 +00:00
commandline	Fix typo and tell people not to post user errors	2010-10-03 18:58:03 +00:00
datasources/pipeline	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
gatk	comment out debugging line that was clogging the performance test output.	2010-10-13 03:26:55 +00:00
oneoffprojects	A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running...	2010-10-12 18:39:56 +00:00
playground	Get rid of useless test/'optimization' that was carried over from UGv1. New codde is (minimally) faster with same results.	2010-10-11 04:04:07 +00:00
queue	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
utils	Experimental code for better filtering of bases in sam records. Not hooked up yet.	2010-10-11 02:19:51 +00:00