Added basic unit tests to sv calling

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

@@ -58,6 +58,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
 
     callers.foreach { caller =>
+      caller.inputBams = inputBams
       caller.outputDir = new File(outputDir, caller.name)
       add(caller)
     }

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

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import java.io.{ File, FileOutputStream }
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerConfig, BreakdancerCaller }
+import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
+import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
+import nl.lumc.sasc.biopet.utils.config.Config
+import nl.lumc.sasc.biopet.extensions.Freebayes
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.extensions.tools.VcfFilter
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
+
+import scala.collection.mutable.ListBuffer
+
+/**
+ * Test class for [[ShivaVariantcalling]]
+ *
+ * Created by pjvan_thof on 3/2/15.
+ */
+class ShivaSvCallingTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): ShivaSvCalling = {
+    new ShivaSvCalling {
+      override def configName = "shivasvcalling"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "shivaSvCallingOptions")
+  def shivaSvCallingOptions = {
+    val bool = Array(true, false)
+    (for (
+      bams <- 0 to 3;
+      delly <- bool;
+      clever <- bool;
+      breakdancer <- bool
+    ) yield Array(bams, delly, clever, breakdancer)).toArray
+  }
+
+  @Test(dataProvider = "shivaSvCallingOptions")
+  def testShivaSvCcalling(bams: Int,
+                          delly: Boolean,
+                          clever: Boolean,
+                          breakdancer: Boolean) = {
+    val callers: ListBuffer[String] = ListBuffer()
+    if (delly) callers.append("delly")
+    if (clever) callers.append("clever")
+    if (breakdancer) callers.append("breakdancer")
+    val map = Map("sv_callers" -> callers.toList)
+    val pipeline = initPipeline(map)
+
+    pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaSvCallingTest.inputTouch("bam_" + n + ".bam")).toMap
+
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!delly && !clever && !breakdancer)
+
+    if (illegalArgumentException) intercept[IllegalArgumentException] {
+      pipeline.init()
+      pipeline.script()
+    }
+
+    if (!illegalArgumentException) {
+      pipeline.init()
+      pipeline.script()
+
+      pipeline.functions.count(_.isInstanceOf[BreakdancerCaller]) shouldBe (if (breakdancer) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[BreakdancerConfig]) shouldBe (if (breakdancer) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[BreakdancerVCF]) shouldBe (if (breakdancer) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[CleverCaller]) shouldBe (if (clever) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[DellyCaller]) shouldBe (if (delly) (bams * 4) else 0)
+
+    }
+  }
+
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(ShivaSvCallingTest.outputDir)
+  }
+}
+
+object ShivaSvCallingTest {
+  val outputDir = Files.createTempDir()
+  new File(outputDir, "input").mkdirs()
+  def inputTouch(name: String): File = {
+    val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+    Files.touch(file)
+    file
+  }
+
+  private def copyFile(name: String): Unit = {
+    val is = getClass.getResourceAsStream("/" + name)
+    val os = new FileOutputStream(new File(outputDir, name))
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+  }
+
+  copyFile("ref.fa")
+  copyFile("ref.dict")
+  copyFile("ref.fa.fai")
+
+  val config = Map(
+    "name_prefix" -> "test",
+    "output_dir" -> outputDir,
+    "cache" -> true,
+    "dir" -> "test",
+    "vep_script" -> "test",
+    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "gatk_jar" -> "test",
+    "samtools" -> Map("exe" -> "test"),
+    "md5sum" -> Map("exe" -> "test"),
+    "bgzip" -> Map("exe" -> "test"),
+    "tabix" -> Map("exe" -> "test"),
+    "breakdancerconfig" -> Map("exe" -> "test"),
+    "breakdancercaller" -> Map("exe" -> "test"),
+    "clever" -> Map("exe" -> "test"),
+    "delly" -> Map("exe" -> "test"),
+    "varscan_jar" -> "test"
+  )
+}
\ No newline at end of file

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

@@ -80,10 +80,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes && !varscanCnsSinglesample)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
+      pipeline.init()
       pipeline.script()
     }
 
     if (!illegalArgumentException) {
+      pipeline.init()
       pipeline.script()
 
       pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe (1 + (if (raw) 1 else 0) + (if (varscanCnsSinglesample) 1 else 0))