Added gears as optional step into mapping

public/mapping/pom.xml

@@ -43,6 +43,11 @@
             <artifactId>Flexiprep</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Gears</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>BamMetrics</artifactId>

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

@@ -19,6 +19,7 @@ import java.io.File
 import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.pipelines.gears.Gears
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
@@ -273,6 +274,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     add(Ln(this, bamFile, finalBamFile))
     outputFiles += ("finalBamFile" -> finalBamFile.getAbsoluteFile)
 
+    if (config("unmapped_to_gears", default = false).asBoolean) {
+      val gears = new Gears(this)
+      gears.bamFile = Some(finalBamFile)
+      gears.outputDir = new File(outputDir, "gears")
+      gears.init()
+      gears.biopetScript()
+      addAll(gears.functions)
+    }
+
     if (config("generate_wig", default = false).asBoolean)
       addAll(Bam2Wig(this, finalBamFile).functions)