fromer 4bec93e3e4 Permit retrieval of read names for debugging purposes ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5011 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-18 16:09:34 +00:00
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analyzeconcordance	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
examples	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
gatk/walkers	Permit retrieval of read names for debugging purposes	2011-01-18 16:09:34 +00:00
sample	Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine	2010-09-17 14:05:26 +00:00
tools	removing unused fastqtobam	2011-01-13 14:29:32 +00:00
utils	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00