BaseRecalibrator.scala 1022 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 BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
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  if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)
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  if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").asString)
  if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)
}

object BaseRecalibrator {
  def apply(root: Configurable, input: File, output: File): BaseRecalibrator = {
    val br = new BaseRecalibrator(root)
    br.input_file :+= input
    br.out = output
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    br.beforeGraph
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    return br
  }
}