Format fixes

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

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 

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

@@ -4,13 +4,13 @@ import java.io.File
 
 import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.utils.ToolCommand
-import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
+import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 
 import scala.collection.JavaConversions._
 
 /**
-  * Created by pjvanthof on 10/12/2016.
-  */
+ * Created by pjvanthof on 10/12/2016.
+ */
 object ValidateVcf extends ToolCommand {
   case class Args(inputVcf: File = null,
                   reference: File = null,

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateVcfTest.scala

@@ -7,8 +7,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 12-12-16.
-  */
+ * Created by pjvan_thof on 12-12-16.
+ */
 class ValidateVcfTest extends TestNGSuite with Matchers {
 
   private def resourcePath(p: String): String =

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.extensions.gatk._
 import nl.lumc.sasc.biopet.extensions.tools.ValidateVcf