Full funcional object now, root need to be in the constructor of class

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -4,10 +4,11 @@ import java.io.File
 import org.broadinstitute.sting.queue.util.Logging
 
 trait Configurable extends Logging {
-  val globalConfig: Config
-  val configPath: List[String]
-  protected var configName = getClass.getSimpleName.toLowerCase
-  protected var configFullPath = configName :: configPath
+  val root: Configurable
+  val globalConfig: Config = if (root != null) root.globalConfig else new Config()
+  val configPath: List[String] = if (root != null) root.configFullPath else List()
+  protected val configName = getClass.getSimpleName.toLowerCase
+  protected val configFullPath = configName :: configPath
   
   def config(key:String) = globalConfig(configName, configPath, key)
   def config(key:String, default:Any) = globalConfig(configName, configPath, key, default)