From b7defeae8315ad39f9b6226af6751a9d81836dec Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 1 Jun 2009 15:50:44 +0000 Subject: [PATCH] Fix bug in unit tests created by new filter in TraversalEngine. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@868 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/traversals/TraversalEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 2d3b16129..f427117f6 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -417,7 +417,7 @@ public abstract class TraversalEngine { if (beSafeP != null && beSafeP && enableVerification) wrappedIterator = new VerifyingSamIterator(wrappedIterator); - if ( filterZeroMappingQualityReads ) + if ( filterZeroMappingQualityReads != null && filterZeroMappingQualityReads ) wrappedIterator = StingSAMIteratorAdapter.adapt(wrappedIterator.getSourceInfo(), new FilteringIterator(wrappedIterator, new ZeroMappingQualityReadFilterFunc()));