asivache 7a11b4f35d Another change in variant classification values ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5237 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-14 17:47:58 +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	Another change in variant classification values	2011-02-14 17:47:58 +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	Updates to handle CG data, headers, etc.	2011-02-08 03:16:05 +00:00
utils	When remapping the read, set MAPQ, CIGAR etc to 0/null for unmapped reads. This is not required according to spec but current samtools jdk otherwise dies in STRICT validation mode.	2011-01-26 19:49:07 +00:00