Mark DePristo a783f19ab1 Fix for potential HaplotypeCaller bug in annotation ordering ... -- Annotations were being called on VariantContext that might needed to be trimmed. Simply inverted the order of operations so trimming occurs before the annotations are added. -- Minor cleanup of call to PairHMM in LikelihoodCalculationEngine		2013-03-20 22:54:35 -04:00
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java	Fix for potential HaplotypeCaller bug in annotation ordering	2013-03-20 22:54:35 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00