From 23ec5b94cf55b4dcc29fac64a4552774abaa97eb Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 4 Aug 2011 09:50:02 -0400 Subject: [PATCH] fixed a missing check for null There was a missed check for the case when you don't provide an indels vcf for the cleaner. --- .../sting/queue/qscripts/DataProcessingPipeline.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index 959d073c7..bef3495bf 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -303,7 +303,7 @@ class DataProcessingPipeline extends QScript { this.out = outIntervals this.mismatchFraction = 0.0 this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) - if (!indels.isEmpty) + if (indels != null) this.rodBind :+= RodBind("indels", "VCF", indels) this.scatterCount = nContigs this.analysisName = queueLogDir + outIntervals + ".target" @@ -315,7 +315,7 @@ class DataProcessingPipeline extends QScript { this.targetIntervals = tIntervals this.out = outBam this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) - if (!qscript.indels.isEmpty) + if (qscript.indels != null) this.rodBind :+= RodBind("indels", "VCF", qscript.indels) this.consensusDeterminationModel = consensusDeterminationModel this.compress = 0