diff --git a/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java b/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java index 4b323632c..bb9e0e3c1 100644 --- a/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java +++ b/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java @@ -77,7 +77,7 @@ public class AnalysisTK extends CommandLineProgram { this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods); engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true")); //engine.testReference(); - + ValidationStringency strictness; if ( STRICTNESS_ARG == null ) { strictness = ValidationStringency.STRICT;