Fixed small issues

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala

@@ -37,6 +37,13 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
   override def defaultThreads = 4
   override def defaultCoreMemory = 4.0
 
+  @Output
+  private var indexOutput: File = _
+
+  override def beforeGraph(): Unit = {
+    indexOutput = new File(output + ".bai")
+  }
+
   /** Returns command to execute */
   def cmdLine: String = required(executable) +
     required("merge") +

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -267,9 +267,11 @@ trait MultisampleMappingTrait extends MultiSampleQScript
             val merge = new SambambaMerge(qscript)
             merge.input = libraries.flatMap(_._2.preProcessBam).toList
             merge.output = mergedBam
+            merge.isIntermediate = true
             add(merge)
           }
           add(SambambaMarkdup(qscript, mergedBam, bamFile.get, isIntermediate = !keepMergedFiles))
+          Ln(qscript, bamFile.get + ".bai", bamFile.get.getAbsolutePath.stripSuffix(".bam") + ".bai")
         case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
       }