Fixed vep config

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
-import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
-import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, LazyCheck, Logging}
+import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
 
 import scala.collection.JavaConversions._
 
@@ -59,7 +59,6 @@ trait Reference extends Configurable {
   lazy val dbsnpVersion: Option[Int] = config("dbsnp_version")
   lazy val dbsnpSubPath: List[String] = dbsnpVersion.map(x => List("dbsnp_annotations", x.toString)).getOrElse(Nil)
   def dbsnpVcfFile: Option[File] = config("dbsnp_vcf", extraSubPath = dbsnpSubPath)
-  lazy val vepConfig: Option[String] = config("vep_config")
 
   /** Returns the reference config path */
   def referenceConfigPath = {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.utils.{ Logging, VcfUtils, tryToParseNumber }
+import nl.lumc.sasc.biopet.utils.{LazyCheck, Logging, VcfUtils, tryToParseNumber}
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 import scala.io.Source
 
@@ -39,7 +39,15 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   @Output(doc = "output file", required = true)
   var output: File = null
 
-  override def subPath = super.subPath ++ vepConfig
+  lazy val vepConfig = new LazyCheck({
+    val s: Option[String] = config("vep_config")
+    s
+  })
+
+  override def subPath = {
+    if (vepConfig.isSet) super.subPath ++ vepConfig()
+    else super.subPath
+  }
 
   def versionRegex = """version (\d*)""".r
   def versionCommand = executable + " " + vepScript + " --help"