Breakdancer.scala 1.01 KB
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package nl.lumc.sasc.biopet.pipelines.shiva.svcallers

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import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerCaller, BreakdancerConfig }
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import nl.lumc.sasc.biopet.utils.config.Configurable

/** Script for sv caler Breakdancer */
class Breakdancer(val root: Configurable) extends SvCaller {
  def name = "breakdancer"

  def biopetScript() {
    for ((sample, bamFile) <- inputBams) {
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      val breakdancerSampleDir = new File(outputDir, sample)

      // read config and set all parameters for the pipeline
      logger.debug("Starting Breakdancer configuration")

      val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
      val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
      val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"))
      add(bdcfg, breakdancer, bdvcf)
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      addVCF(sample, bdvcf.output)
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    }
  }
}