Moved the check of Alternate bases to the checkPreconditions function

app/node-app/arraymap-beacon/v0.3/beacon-query.js

@@ -72,7 +72,14 @@ function checkPreconditions(params) {
     if (!params.alternateBases) {
         return {
             hasError: true,
-            msg: "variant class is not defined, arrayMap supports be DUP or DEL"
+            msg: "Alternate bases not defined, arrayMap supports DUP or DEL"
+        };
+    }
+
+    if (!alternateBasesMap[params.alternateBases]) {
+        return {
+            hasError: true,
+            msg: "Alternate bases not supported, arrayMap supports DUP or DEL"
         };
     }
 
@@ -115,8 +122,6 @@ function buildMongoQuery(params) {
     var andConditions = [];
     var orConditions  = [];
 
-    if (alternateBasesMap[params.alternateBases]) {
-
     //add constraint on datasets if required
     if (params.datasetIds) {
         if (params.datasetIds != 'all') {
@@ -159,7 +164,6 @@ function buildMongoQuery(params) {
     if (orConditions.length > 0) {
         andConditions.push({$or: orConditions});
     }
-    }
 
     return {
         $and: andConditions