autostyle changes

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala

@@ -4,11 +4,11 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.ToolCommandFunction
 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 24-11-16.
-  */
+ * Created by Sander Bollen on 24-11-16.
+ */
 class XcnvToBed(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.XcnvToBed
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala

 package nl.lumc.sasc.biopet.tools
 
-import java.io.{BufferedWriter, File, FileWriter}
+import java.io.{ BufferedWriter, File, FileWriter }
 
 import nl.lumc.sasc.biopet.tools.VepNormalizer.Args
 import nl.lumc.sasc.biopet.utils.ToolCommand
@@ -8,8 +8,8 @@ import nl.lumc.sasc.biopet.utils.ToolCommand
 import scala.io.Source
 
 /**
-  * Created by Sander Bollen on 24-11-16.
-  */
+ * Created by Sander Bollen on 24-11-16.
+ */
 object XcnvToBed extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
@@ -17,7 +17,6 @@ object XcnvToBed extends ToolCommand {
       .parse(args, Args())
       .getOrElse(throw new IllegalArgumentException)
 
-
     val writer = new BufferedWriter(new FileWriter(commandArgs.outputBed))
     Source.fromFile(commandArgs.inputXcnv).
       getLines().
@@ -46,7 +45,7 @@ object XcnvToBed extends ToolCommand {
     }
   }
 
-  case class Args(inputXcnv: File = null, outputBed: File = null , sample: String = null) extends AbstractArgs
+  case class Args(inputXcnv: File = null, outputBed: File = null, sample: String = null) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     head("Convert a sample track within an XHMM XCNV file to a BED track. Fourt column indicates deletion (-1), normal (0) or duplication (1) of region")
@@ -58,12 +57,12 @@ object XcnvToBed extends ToolCommand {
     } text {
       "Input XCNV file"
     }
-    opt[File]('O', "Output") required() valueName "<bed>" action { (x,c) =>
+    opt[File]('O', "Output") required () valueName "<bed>" action { (x, c) =>
       c.copy(outputBed = x)
     } text {
       "Output BED file"
     }
-    opt[String]('S', "Sample") required() action { (x,c) =>
+    opt[String]('S', "Sample") required () action { (x, c) =>
       c.copy(sample = x)
     } text {
       "The sample which to select"

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

@@ -101,7 +101,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
 
     // create bed files
     val bedDir = new File(xhmmDir, "beds")
-    val beds = inputBams.keys.map{ x =>
+    val beds = inputBams.keys.map { x =>
       val z = new XcnvToBed(this)
       z.inputXcnv = discover.outputXcnv
       z.sample = x