SvCaller.scala 785 Bytes
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package nl.lumc.sasc.biopet.pipelines.shiva.svcallers

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import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript }
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import org.broadinstitute.gatk.queue.QScript

/**
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 * Created by pjvanthof on 23/11/15.
 */
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trait SvCaller extends QScript with BiopetQScript with Reference {

  /** Name of mode, this should also be used in the config */
  def name: String

  var namePrefix: String = _

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  var inputBams: Map[String, File] = Map.empty
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  def outputVCF(sample: String): Option[File] = {
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    outputVCFs.get(sample) match {
      case Some(file) => Some(file)
      case _          => None
    }
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  }

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  protected var outputVCFs: Map[String, File] = Map.empty
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  protected def addVCF(sampleId: String, outputVCF: File) = {
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    outputVCFs += (sampleId -> outputVCF)
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  }

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  def init() = {}
}