Fix multiple bugs

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -4,6 +4,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.tools.{ VcfFilter, MpileupToVcf }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.Input
@@ -19,30 +20,45 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
   var inputBams: List[File] = Nil
 
-  def init: Unit = {
+  var namePrefix: String = ""
 
+  def init: Unit = {
+    if (!namePrefix.isEmpty && !namePrefix.endsWith(".")) namePrefix += "."
   }
 
   def biopetScript: Unit = {
+    val cv = new CombineVariants(qscript)
+    cv.outputFile = new File(outputDir, namePrefix + ".final.vcf.gz")
+    for (caller <- callers) {
+      caller.addJobs()
+      cv.addInput(caller.outputFile, caller.name)
+    }
+    add(cv)
+
     addSummaryJobs
   }
 
+  def callers = List(new RawVcf).filter(_.use)
+
   trait Variantcaller {
     val name: String
     def outputDir = new File(qscript.outputDir, name)
-    val defaultUse: Boolean
-    val use: Boolean = config("use_" + name, default = defaultUse)
-    val defaultPrio: Int
-    val prio: Int = config("prio_" + name, default = defaultPrio)
-    def addJobs(): File
+    protected val defaultUse: Boolean
+    lazy val use: Boolean = config("use_" + name, default = defaultUse)
+    protected val defaultPrio: Int
+    lazy val prio: Int = config("prio_" + name, default = defaultPrio)
+    def addJobs()
+    def outputFile: File
   }
 
   class RawVcf extends Variantcaller {
     val name = "raw"
-    val defaultPrio = 999
-    val defaultUse = true
+    protected val defaultPrio = 999
+    protected val defaultUse = true
+
+    def outputFile = new File(outputDir, namePrefix + "raw.vcf.gz")
 
-    def addJobs(): File = {
+    def addJobs() {
       val rawFiles = inputBams.map(bamFile => {
         val m2v = new MpileupToVcf(qscript)
         m2v.inputBam = bamFile
@@ -63,8 +79,10 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
         vcfFilter.outputVcf
       })
 
-      //TODO: Combine variants
-      null
+      val cv = new CombineVariants(qscript)
+      cv.inputFiles = rawFiles
+      cv.outputFile = outputFile
+      add(cv)
     }
   }