Change tests to accept pindel

Add testcode to accept merged VCFs

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala

@@ -19,7 +19,7 @@ class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
   var flanking: Option[Int] = config("flanking")
 
   var exclusionRegions: List[File] = config("exclusion_regions")
-  var translocationsOnly: Boolean = config("translocations_only")
+  var translocationsOnly: Boolean = config("translocations_only", default = false)
 
   @Output(doc = "Unzipped file", required = true)
   var output: File = _

public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala

@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.utils
 import java.io.File
 
 import htsjdk.samtools._
-import org.mockito.Mockito.{ inOrder => inOrd }
+import org.mockito.Mockito.{inOrder => inOrd}
 import org.scalatest.Matchers
 import org.scalatest.mock.MockitoSugar
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ BeforeClass, Test }
+import org.testng.annotations.{BeforeClass, Test}
 
 /**
  * Created by wyleung on 22-2-16.

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

@@ -18,9 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.Pysvtools
-import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Breakdancer, Clever, Delly, SvCaller }
-import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
-import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Breakdancer, Clever, Delly, SvCaller, _ }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
@@ -68,12 +66,12 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
 
     // merge VCF by sample
     for ((sample, bamFile) <- inputBams) {
-      var sampleVcfs: List[File] = List()
+      var sampleVCFS: List[Option[File]] = List.empty
       callers.foreach { caller =>
-        sampleVcfs :+= caller.outputVCF(sample).get
+        sampleVCFS ::= caller.outputVCF(sample)
       }
       val mergeSVcalls = new Pysvtools(this)
-      mergeSVcalls.input = sampleVcfs
+      mergeSVcalls.input = sampleVCFS.flatten
       mergeSVcalls.output = new File(outputDir, sample + ".merged.vcf")
       add(mergeSVcalls)
       //      outputFiles += (sample -> mergeSVcalls.output)

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

@@ -57,6 +57,8 @@ class Pindel(val root: Configurable) extends SvCaller {
       pindelVcf.rDate = todayformat.format(today) // officially, we should enter the date of the genome here
       pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
       add(pindelVcf)
+
+      addVCF(sample, pindelVcf.outputVCF)
     }
 
   }

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

@@ -13,16 +13,19 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
 
   var namePrefix: String = _
 
-  var inputBams: Map[String, File] = _
+  var inputBams: Map[String, File] = Map.empty
 
   def outputVCF(sample: String): Option[File] = {
-    outputVcfs.get(sample)
+    outputVCFs.get(sample) match {
+      case Some(file) => Some(file)
+      case _          => None
+    }
   }
 
-  protected var outputVcfs: Map[String, File] = _
+  protected var outputVCFs: Map[String, File] = Map.empty
 
   protected def addVCF(sampleId: String, outputVCF: File) = {
-    outputVcfs += (sampleId -> outputVCF)
+    outputVCFs += (sampleId -> outputVCF)
   }
 
   def init() = {}

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala

@@ -221,6 +221,10 @@ object ShivaSvCallingTest {
     "pindelvcf" -> Map("exe" -> "test"),
     "clever" -> Map("exe" -> "test"),
     "delly" -> Map("exe" -> "test"),
-    "varscan_jar" -> "test"
+    "varscan_jar" -> "test",
+    "pysvtools" -> Map(
+      "exe" -> "test",
+      "exclusion_regions" -> "test",
+      "translocations_only" -> false)
   )
 }
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