Added gears to multi mapping

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -264,11 +264,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     if (config("unmapped_to_gears", default = false).asBoolean) {
       val gears = new GearsSingle(this)
       gears.bamFile = Some(finalBamFile)
+      gears.sampleId = sampleId
+      gears.libId = libId
       gears.outputDir = new File(outputDir, "gears")
-      gears.init()
-      gears.biopetScript()
-      addAll(gears.functions)
-      addSummaryQScript(gears)
+      add(gears)
     }
 
     if (config("generate_wig", default = false).asBoolean)

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala

@@ -8,6 +8,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, MultiSampleQScript
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles, AddOrReplaceReadGroups, SamToFastq }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
+import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
@@ -199,6 +200,14 @@ trait MultisampleMappingTrait extends MultiSampleQScript
         bamMetrics.outputDir = new File(sampleDir, "metrics")
         add(bamMetrics)
       }
+
+      if (config("unmapped_to_gears", default = false) && libraries.flatMap(_._2.bamFile).nonEmpty) {
+        val gears = new GearsSingle(qscript)
+        gears.bamFile = preProcessBam
+        gears.sampleId = Some(sampleId)
+        gears.outputDir = new File(sampleDir, "gears")
+        add(gears)
+      }
     }
   }
 }