Adding metrics step on merged bam file

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

@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
 import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
@@ -108,6 +109,9 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
         add(merge)
       }
 
+      val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"))
+      addAll(bamMetrics.functions)
+      addSummaryQScript(bamMetrics)
       addAll(Bam2Wig(qscript, bamFile).functions)
 
       val macs2 = new Macs2CallPeak(qscript)