Fixing stackoverflow

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

@@ -101,12 +101,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
       lazy val bamToFastq: Boolean = config("bam_to_fastq", default = false)
       lazy val correctReadgroups: Boolean = config("correct_readgroups", default = false)
 
+      def keepFinalBamfile = samples(sampleId).libraries.size == 1
+
       lazy val mapping: Option[Mapping] = if (inputR1.isDefined || (inputBam.isDefined && bamToFastq)) {
         val m: Mapping = new Mapping(qscript) {
           override def configNamespace = "mapping"
           override def defaults: Map[String, Any] = super.defaults ++
-            Map("keep_final_bamfile" -> !(samples(lib.sampleId).libraries.size > 1 ||
-              preProcessBam.map(_ != bamFile).getOrElse(false)))
+            Map("keep_final_bamfile" -> keepFinalBamfile)
         }
         m.sampleId = Some(sampleId)
         m.libId = Some(libId)

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala

@@ -86,6 +86,8 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
         c && br.knownSites.nonEmpty
       }
 
+      override def keepFinalBamfile = super.keepFinalBamfile && !useIndelRealigner && !useBaseRecalibration
+
       override def preProcessBam = if (useIndelRealigner && useBaseRecalibration)
         bamFile.map(swapExt(libDir, _, ".bam", ".realign.baserecal.bam"))
       else if (useIndelRealigner) bamFile.map(swapExt(libDir, _, ".bam", ".realign.bam"))