From b19fd4d45cc28bfe8c414d66fbcc22f6458716e6 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 18 Sep 2009 17:10:49 +0000 Subject: [PATCH] Damn unit tests have a null Toolkit()... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1654 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/CleanedReadInjector.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java index b7be6de2e..206592adf 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java @@ -74,7 +74,8 @@ public class CleanedReadInjector extends ReadWalker { // If there are intervals specified by the user,record them so we can make sure not // to emit reads outside the intervals. For now, we'll group them by chromosome to // make lookup a bit faster. - if ( this.getToolkit().getArguments().intervals != null ) { + if ( this.getToolkit() != null && + this.getToolkit().getArguments().intervals != null ) { intervals = new HashMap>(); List locs = GenomeAnalysisEngine.parseIntervalRegion(this.getToolkit().getArguments().intervals); Iterator iter = GenomeLocSortedSet.createSetFromList(locs).iterator();