style changes, bamMetrics changed in bammetrics

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala

@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.extensions.picard
 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.{ Output, Input }
 
 /**
  * Created by sajvanderzeeuw on 6-10-15.
  */
-class BuildBamIndex (val root: Configurable) extends Picard {
+class BuildBamIndex(val root: Configurable) extends Picard {
 
   javaMainClass = new picard.sam.BuildBamIndex().getClass.getName
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
 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 pjvanthof on 22/09/15.

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -127,7 +127,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
 
       val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
       addAll(bamMetricsFilter.functions)
-      bamMetricsFilter.summaryName = "bamMetrics-filter"
+      bamMetricsFilter.summaryName = "bammetrics-filter"
       addSummaryQScript(bamMetricsFilter)
 
       addAll(Bam2Wig(qscript, bamFile).functions)