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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.
This commit is contained in:
Mauricio Carneiro 2011-08-04 09:50:02 -04:00
parent a587f38808
commit 23ec5b94cf
1 changed files with 2 additions and 2 deletions
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4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -303,7 +303,7 @@ class DataProcessingPipeline extends QScript {
this.out = outIntervals this.out = outIntervals
this.mismatchFraction = 0.0 this.mismatchFraction = 0.0
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
if (!indels.isEmpty) if (indels != null)
this.rodBind :+= RodBind("indels", "VCF", indels) this.rodBind :+= RodBind("indels", "VCF", indels)
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outIntervals + ".target" this.analysisName = queueLogDir + outIntervals + ".target"
@ -315,7 +315,7 @@ class DataProcessingPipeline extends QScript {
this.targetIntervals = tIntervals this.targetIntervals = tIntervals
this.out = outBam this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
if (!qscript.indels.isEmpty) if (qscript.indels != null)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels) this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.consensusDeterminationModel = consensusDeterminationModel this.consensusDeterminationModel = consensusDeterminationModel
this.compress = 0 this.compress = 0