Commit bf514e93 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove unused trait

parent ff0d656a
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 }
}
}
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