style fixes

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

@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
 
   def analysis_type = "DepthOfCoverage"
@@ -26,7 +26,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
     new File(out + "_summary")
   }
 
-  lazy val statisticsFile:File = {
+  lazy val statisticsFile: File = {
     new File(out + "_statistics")
   }
 
@@ -117,7 +117,6 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
   @Argument(required = false)
   var printBinEndpointsAndExit: Boolean = false
 
-
   override def cmdLine = {
     super.cmdLine + required("--out", out) +
       optional("--calculateCoverageOverGenes", calculateCoveraOverGenes) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala

 package nl.lumc.sasc.biopet.extensions.xhmm
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  *
-  * Generic abstract class for XHMM commands
-  */
-abstract class Xhmm extends BiopetCommandLineFunction with Version  {
+ * Created by Sander Bollen on 23-11-16.
+ *
+ * Generic abstract class for XHMM commands
+ */
+abstract class Xhmm extends BiopetCommandLineFunction with Version {
 
   executable = config("exe", namespace = "xhmm", default = "xhmm")
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala

@@ -4,13 +4,13 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 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 }
 
 import scala.io.Source
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
 
   @Input
@@ -53,7 +53,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
       map(x => XcnvLine(x(0), x(1), x(2))).toList
 
     val samples = lines.map(_.sample)
-    samples.map{x =>
+    samples.map { x =>
       val sampleLines = lines.filter(_.sample == x)
       x -> Map(
         "DEL" -> sampleLines.count(_.cnvType == "DEL"),

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala

@@ -4,11 +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 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
 
   @Input
@@ -24,7 +24,7 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
   var r: File = _
 
   @Argument
-  var discoverParamsFile: File =  config("discover_params", namespace = "xhmm")
+  var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
 
   def cmdLine = {
     executable + required("--genotype") +
@@ -36,6 +36,4 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
       required("-v", outputVcf)
   }
 
-
-
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala

@@ -3,12 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
 import java.io.File
 
 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 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmMatrix(val root: Configurable) extends Xhmm {
 
   @Input

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala

@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmMergeGatkDepths(val root: Configurable) extends Xhmm {
 
   @Input(doc = "List of input depths files")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala

@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
 import java.io.File
 
 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 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmNormalize(val root: Configurable) extends Xhmm {
 
   @Input

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala

@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmPca(val root: Configurable) extends Xhmm {
 
   @Input

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

@@ -9,8 +9,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmTest extends TestNGSuite with Matchers {
 
   @Test

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala

@@ -15,9 +15,9 @@
 package nl.lumc.sasc.biopet.pipelines.kopisu
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
-import nl.lumc.sasc.biopet.pipelines.kopisu.methods.{CnmopsMethod, ConiferMethod, FreecMethod, XhmmMethod}
-import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
+import nl.lumc.sasc.biopet.pipelines.kopisu.methods.{ CnmopsMethod, ConiferMethod, FreecMethod, XhmmMethod }
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -75,7 +75,7 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
       add(method)
     }
 
-    xhmmMethod.foreach{ method =>
+    xhmmMethod.foreach { method =>
       method.inputBams = inputBams
       method.outputDir = new File(outputDir, "xhmm_methid")
     }

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala

@@ -6,8 +6,8 @@ import nl.lumc.sasc.biopet.extensions.xhmm._
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /**
-  * Created by Sander Bollen on 23-11-16.
-  */
+ * Created by Sander Bollen on 23-11-16.
+ */
 class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
 
   def name = "xhmm"