diff --git a/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java index 225cac013..9ca8dadeb 100755 --- a/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java +++ b/playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java @@ -315,7 +315,7 @@ public class TraversalEngine { if ( SORT_ON_FLY ) samReadIter = new SortSamIterator(samReadIter, MAX_ON_FLY_SORTS); - else if ( beSafeP ) + if ( beSafeP ) samReadIter = new VerifyingSamIterator(samReadIter); if ( THREADED_IO ) {