Register GATK-full-only walkers and rethrow the missing walker error as a not supported in GATK lite error

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -281,7 +281,14 @@ public class GenomeAnalysisEngine {
      * @return An instance of the walker.
      */
     public Walker<?, ?> getWalkerByName(String walkerName) {
+        try {
             return walkerManager.createByName(walkerName);
+        } catch ( UserException e ) {
+            if ( isGATKLite() && GATKLiteUtils.isAvailableOnlyInFullGATK(walkerName) ) {
+                e = new UserException.NotSupportedInGATKLite("the " + walkerName + " walker is available only in the full version of the GATK");
+            }
+            throw e;
+        }
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java

@@ -41,6 +41,21 @@ public class GATKLiteUtils {
      */
     private GATKLiteUtils() { }
 
+
+    private static Set<String> fullVersionGATKWalkers = new HashSet<String>();
+    static {
+        fullVersionGATKWalkers.add("HaplotypeCaller");
+        fullVersionGATKWalkers.add("ReduceReads");
+    }
+    /**
+     * Utility method to check whether a given walker is only available in the full GATK release
+     *
+     * @param walkerName   the walker class name (not the package) to check
+     */
+    public static boolean isAvailableOnlyInFullGATK(final String walkerName) {
+        return fullVersionGATKWalkers.contains(walkerName);
+    }
+
     /**
      * Utility method to determine whether this is the lite version of the GATK
      */

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -80,7 +80,7 @@ public class UserException extends ReviewedStingException {
 
     public static class NotSupportedInGATKLite extends UserException {
         public NotSupportedInGATKLite(String message) {
-            super(String.format("GATK Lite does support all of the features of the full version: %s", message));
+            super(String.format("GATK Lite does not support all of the features of the full version: %s", message));
         }
     }