Reading of config files now in BiopetExecutable

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

 package nl.lumc.sasc.biopet.core
 
+import java.io.File
 import java.util.Properties
+import nl.lumc.sasc.biopet.core.config.Config
 import org.apache.log4j.Logger
 
 object BiopetExecutable extends Logging {
@@ -82,6 +84,11 @@ object BiopetExecutable extends Logging {
       return command.get
     }
 
+    // Read config files
+    for (t <- 0 until args.size) {
+      if (args(t) == "-config" || args(t) == "--config_ile") Config.global.loadConfigFile(new File(args(t + 1)))
+    }
+
     args match {
       case Array("version") => {
         println("version: " + getVersion)

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

@@ -25,7 +25,6 @@ trait BiopetQScript extends Configurable {
   var functions: Seq[QFunction]
 
   final def script() {
-    for (file <- configfiles) Config.global.loadConfigFile(file)
     if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript