Commit 5d9d3661 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix format

parent bedfafee
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 2/26/15.
......@@ -24,7 +24,7 @@ class CombineVariants(val root: Configurable) extends Gatk {
var inputMap: Map[File, String] = Map()
def addInput(file:File, name:String): Unit = {
def addInput(file: File, name: String): Unit = {
inputFiles :+= file
inputMap += file -> name
}
......@@ -40,8 +40,9 @@ class CombineVariants(val root: Configurable) extends Gatk {
(for (file <- inputFiles) yield {
inputMap.get(file) match {
case Some(name) => required("--variant:" + name, file)
case _ => required("--variant", file)
}}).mkString +
case _ => required("--variant", file)
}
}).mkString +
required("-o", outputFile) +
optional("--setKey", setKey) +
(if (rodPriorityList.isEmpty) "" else optional("--rod_priority_list", rodPriorityList.mkString(","))) +
......
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