Merge remote-tracking branch 'origin/feature-VarscanIntoShiva' into feature-VarscanIntoShiva

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

@@ -15,20 +15,15 @@
  */
 package nl.lumc.sasc.biopet.extensions.varscan
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetJavaCommandLineFunction }
 
-abstract class Varscan extends BiopetJavaCommandLineFunction {
+abstract class Varscan extends BiopetJavaCommandLineFunction with Version {
 
   override def subPath = "varscan" :: super.subPath
 
   jarFile = config("varscan_jar")
 
-  /**
-   * TODO: test version
-   * override def versionCommand = super.commandLine
-   * override val versionRegex = """VarScan v(.*)""".r
-   */
-
-  override def defaultCoreMemory = 5.0
+  def versionCommand = super.commandLine
+  def versionRegex = """VarScan v(.*)""".r
 }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala

@@ -39,6 +39,8 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan {
   var vcfSampleList: Option[File] = config("vcf_sample_list")
   var variants: Option[Int] = config("variants")
 
+  override def defaultCoreMemory = 6.0
+
   override def beforeGraph(): Unit = {
     val validValues: Set[Int] = Set(0, 1)
     // check for boolean vars that are passed as ints

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

@@ -5,7 +5,7 @@ import java.io.PrintWriter
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.extensions.varscan.{ FixMpileup, VarscanMpileup2cns }
-import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /**

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

@@ -77,7 +77,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
 
     pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
 
-    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes)
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes && !varscanCnsSinglesample)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()
@@ -86,7 +86,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     if (!illegalArgumentException) {
       pipeline.script()
 
-      pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
+      pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe (1 + (if (raw) 1 else 0) + (if (varscanCnsSinglesample) 1 else 0))
       //pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
       //FIXME: Can not check for bcftools because of piping
       pipeline.functions.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
@@ -133,6 +133,7 @@ object ShivaVariantcallingTest {
     "freebayes" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test"),
     "bgzip" -> Map("exe" -> "test"),
-    "tabix" -> Map("exe" -> "test")
+    "tabix" -> Map("exe" -> "test"),
+    "varscan_jar" -> "test"
   )
 }
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