From 608948210cdc2c0412c7af68682ba02e97df28d0 Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 12 May 2009 13:29:44 +0000 Subject: [PATCH] Check for a reference before extraction. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@661 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/traversals/TraverseReads.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index c0f895f09..a83b64730 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -106,7 +106,8 @@ public class TraverseReads extends TraversalEngine { locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0)); // get the array of characters for the reference sequence, since we're a mapped read - refSeq = dataProvider.getReferenceForRead( read ); + if( dataProvider.hasReference() ) + refSeq = dataProvider.getReferenceForRead( read ); } // update the number of reads we've seen