Optimize imports

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -5,10 +5,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
 import scala.util.Random
 
 class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with BiopetQScript {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -5,11 +5,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ SelectVariants, GenotypeGVCFs }
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -5,20 +5,18 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.MultiSampleQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
 import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineVariants, CombineGVCFs }
-import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
-import scala.collection.JavaConversions._
-import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
-import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineGVCFs, CombineVariants }
+import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
+import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Argument }
+
+import scala.collection.JavaConversions._
 
 class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
   qscript =>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

@@ -5,8 +5,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.BiopetQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
 import org.broadinstitute.gatk.queue.QScript

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -5,17 +5,18 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter, MergeAlleles }
-import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
+import nl.lumc.sasc.biopet.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
 import scala.collection.SortedMap
 import scala.language.reflectiveCalls
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaTrait }
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrait }
 import org.broadinstitute.gatk.queue.QScript
 
 /**