Merge pull request #85 from biopet/fix-BIOPET-661

Fixed bam input

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

@@ -105,8 +105,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
 
       override def keepFinalBamfile: Boolean = super.keepFinalBamfile && !useIndelRealigner && !useBaseRecalibration
 
-      override def bamFile: Option[Mapping#File] = mapping.map(_.mergedBamFile)
-
       override def preProcessBam: Option[Mapping#File] = if (useIndelRealigner && usePrintReads && useBaseRecalibration)
         bamFile.map(swapExt(libDir, _, ".bam", ".realign.baserecal.bam"))
       else if (useIndelRealigner) bamFile.map(swapExt(libDir, _, ".bam", ".realign.bam"))
@@ -189,7 +187,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
       Some(makeVariantcalling(multisample = false, sample = Some(sampleId)))
     } else None
 
-    override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
+    override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner || (libraries.size == 1))
 
     lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)