Commit 661c7456 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix bug on VariantEval -L option

parent 1f80f95b
......@@ -4,9 +4,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
import org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants
import org.broadinstitute.gatk.queue.extensions.gatk.VariantEval
import org.broadinstitute.gatk.queue.extensions.gatk.{ CommandLineGATK, SelectVariants, VariantEval }
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQScript {
......@@ -69,7 +67,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
variantEval.ST = Seq("VariantType", "CompRod")
variantEval.noEV = true
variantEval.EV = Seq("CompOverlap")
if (targetBed != null) variantEval.L = Seq(targetBed)
if (targetBed != null) variantEval.L = targetBed
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