Fix sample bamMetrics

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -186,8 +186,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
 object BamMetrics extends PipelineCommand {
   /** Make default implementation of BamMetrics and runs script already */
-  def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = {
+  def apply(root: Configurable,
+            bamFile: File, outputDir: File,
+            sampleId: Option[String] = None,
+            libId: Option[String] = None): BamMetrics = {
     val bamMetrics = new BamMetrics(root)
+    bamMetrics.sampleId = sampleId
+    bamMetrics.libId = libId
     bamMetrics.inputBam = bamFile
     bamMetrics.outputDir = outputDir
 

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

@@ -107,7 +107,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
         add(merge)
       }
 
-      val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"))
+      val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
       addAll(bamMetrics.functions)
       addSummaryQScript(bamMetrics)
       addAll(Bam2Wig(qscript, bamFile).functions)