Remove unused trait

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

-package nl.lumc.sasc.biopet.extensions.gatk.broad
-
-import nl.lumc.sasc.biopet.core._
-import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
-
-/**
- * @deprecated
- */
-trait GatkGeneral extends org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK with CommandLineResources with Reference with Version {
-  var executable: String = config("java", default = "java", namespace = "java", freeVar = false)
-
-  override def subPath = "gatk" :: super.subPath
-
-  jarFile = config("gatk_jar")
-
-  reference_sequence = referenceFasta()
-
-  override def defaultCoreMemory = 4.0
-  override def faiRequired = true
-  override def dictRequired = true
-
-  if (config.contains("intervals")) intervals = config("intervals").asFileList
-  if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
-
-  Option(config("et").value) match {
-    case Some("NO_ET")  => et = GATKRunReport.PhoneHomeOption.NO_ET
-    case Some("AWS")    => et = GATKRunReport.PhoneHomeOption.AWS
-    case Some("STDOUT") => et = GATKRunReport.PhoneHomeOption.STDOUT
-    case Some(x)        => throw new IllegalArgumentException(s"Unknown et option for gatk: $x")
-    case _              =>
-  }
-
-  if (config.contains("gatk_key")) gatk_key = config("gatk_key")
-  if (config.contains("pedigree")) pedigree = config("pedigree")
-
-  def versionRegex = """(.*)""".r
-  override def versionExitcode = List(0, 1)
-  def versionCommand = "java" + " -jar " + jarFile + " -version"
-
-  override def getVersion = {
-    BiopetCommandLineFunction.preProcessExecutable(executable).path.foreach(executable = _)
-    super.getVersion.collect { case v => "Gatk " + v }
-  }
-}