Change key sets

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

@@ -275,12 +275,12 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     else Map()
   }
 
-  protected val removeOnConflict = Set("Output_file", "Command_line_options", "Run_time", "Start_time", "End_time", "Input_file_(format)", "Novel_/_existing_variants")
-  protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species")
+  protected val removeOnConflict = Set("Output_file", "Run_time", "Start_time", "End_time", "Novel_/_existing_variants")
+  protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species", "Command_line_options", "Input_file_(format)")
 
   override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     if (removeOnConflict.contains(key)) None
-    else if (nonNumber.contains(key)) v1
+    else if (nonNumber.contains(key)) v2
     else {
       (v1, v2) match {
         case (x1: Int, x2: Int) => x1 + x2