Commit bddec662 authored by Sander Bollen's avatar Sander Bollen

autostyle fixes

parent 2fcad6ab
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.tarmac
import java.io.File
import nl.lumc.sasc.biopet.core.{PedigreeQscript, PipelineCommand, Reference}
import nl.lumc.sasc.biopet.core.{ PedigreeQscript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage
......@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function.QFunction
import scalaz.{-\/, \/, \/-}
import scalaz.{ -\/, \/, \/- }
/**
* Created by Sander Bollen on 23-3-17.
......@@ -70,9 +70,9 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
/* Get count file for Xhmm method */
lazy val outputXhmmCountFile: String \/ File = {
outputXhmmCountJob match {
case \/-(ln: Ln) => \/-(ln.output)
case \/-(ln: Ln) => \/-(ln.output)
case \/-(doc: DepthOfCoverage) => \/-(doc.out)
case _ => _
case -\/(error) => -\/(error)
}
}
......@@ -107,17 +107,17 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
/* Get count file for wisecondor method */
lazy val outputWisecondorCountFile: String \/ File = {
outputWisecondorCountJob match {
case \/-(ln: Ln) => \/-(ln.output)
case \/-(ln: Ln) => \/-(ln.output)
case \/-(count: WisecondorCount) => \/-(count.output)
case _ => _
case -\/(error) => -\/(error)
}
}
/** Function to add sample jobs */
def addJobs(): Unit = {
(outputWisecondorCountJob :: outputXhmmCountJob :: Nil).foreach {
case -\/(error) => Logging.addError(error)
case \/-(function) => add(function)
case -\/(error) => Logging.addError(error)
case \/-(function) => add(function)
}
}
......
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