IndelRealigner.scala 936 Bytes
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/**
 * Due to the license issue with GATK, this part of Biopet can only be used inside the
 * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
 * on how to use this protected part of biopet or contact us at sasc@lumc.nl
 */
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package nl.lumc.sasc.biopet.extensions.gatk.broad
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import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable

class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
  if (config.contains("scattercount")) scatterCount = config("scattercount")
}

object IndelRealigner {
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  def apply(root: Configurable, input: File, targetIntervals: File, outputDir: File): IndelRealigner = {
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    val ir = new IndelRealigner(root)
    ir.input_file :+= input
    ir.targetIntervals = targetIntervals
    ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
    return ir
  }
}