autostyle fixes

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -18,17 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.annotations.{ AnnotationRefFlat, RibosomalRefFlat }
-import nl.lumc.sasc.biopet.core.annotations.{AnnotationRefFlat, RibosomalRefFlat}
-import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
-import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag}
-import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort}
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort }
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
-import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
 import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedCheck
 import org.broadinstitute.gatk.queue.QScript
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -84,9 +84,9 @@ object BedtoolsCoverage {
   }
 
   /**
-    * Creates the genome file. i.e. the first two columns of the fasta index
-    * @return
-    */
+   * Creates the genome file. i.e. the first two columns of the fasta index
+   * @return
+   */
   def createGenomeFile(fai: File, dir: File): File = {
     val tmp = File.createTempFile(fai.getName, ".genome", dir)
     tmp.deleteOnExit()

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala

@@ -4,12 +4,11 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
-
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
-  * Created by Sander Bollen on 26-5-16.
-  */
+ * Created by Sander Bollen on 26-5-16.
+ */
 class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
 
   @Input
@@ -21,9 +20,8 @@ class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
   @Argument(required = false)
   var faidx: File = referenceFai
 
-
   def cmdLine = required(executable) + required("sort") + required("-i", input) +
     optional("-faidx", faidx) +
-    (if(outputAsStsout) "" else " > " + required(output))
+    (if (outputAsStsout) "" else " > " + required(output))
 
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala

@@ -118,7 +118,7 @@ object CleverFixVCF extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val input: File = commandArgs.inputVCF
     val output: File = commandArgs.outputVCF

biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala

@@ -4,7 +4,7 @@ import java.io.File
 import java.nio.file.Paths
 
 import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
-import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
@@ -21,7 +21,7 @@ class BedToolsTest extends TestNGSuite with Matchers {
     val file = new File(Paths.get(this.getClass.getResource("/ref.fa.fai").toURI).toString)
     val tmp = File.createTempFile("test", ".bed")
     tmp.deleteOnExit()
-    class TestCov(override val root: Configurable) extends BedtoolsCoverage(root)  {
+    class TestCov(override val root: Configurable) extends BedtoolsCoverage(root) {
       jobTempDir = tmp
       override def referenceFai = file