Fixed defaults

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

@@ -58,7 +58,7 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
   var sexColumn: Option[String] = config("sex_column")
   var stratifyOn: Option[String] = config("stratify_on")
 
-  var conditionOn: List[String] = config("condition_on")
+  var conditionOn: List[String] = config("condition_on", default = Nil)
 
   var priorAdd: List[String] = config("prior_add", default = Nil)
   var priorCov: List[String] = config("prior_cov", default = Nil)
@@ -90,8 +90,8 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
   var range: List[String] = config("range", default = Nil)
   var renorm: Boolean = config("renorm", default = false)
   var snpid: List[String] = config("snpid", default = Nil)
-  var useRawCovariates: Boolean = config("use_raw_covariates")
-  var useRawPhenotypes: Boolean = config("use_raw_phenotypes")
+  var useRawCovariates: Boolean = config("use_raw_covariates", default = false)
+  var useRawPhenotypes: Boolean = config("use_raw_phenotypes", default = false)
   var noClobber: Boolean = config("no_clobber", default = false)
 
   executable = config("exe", default = "snptest")

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

@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  *