Created new DeprecatedToolChecks class

--Based on existing code in GenomeAnalysisEngine
	--Hashmaps hold mapping of deprecated tool name to version number and recommended replacement (if any)
	--Using FastUtils for maps; specifically Object2ObjectMap but there could be a better type for Strings...
	--Added user exception for deprecated annotations
	--Added deprecation check to AnnotationInterfaceManager.validateAnnotations
	--Run when annotations are initialized
	--Made annotation sets instead of lists

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

@@ -67,6 +67,9 @@ import java.io.File;
 import java.util.*;
 import java.util.concurrent.TimeUnit;
 
+import static org.broadinstitute.sting.utils.DeprecatedToolChecks.getWalkerDeprecationInfo;
+import static org.broadinstitute.sting.utils.DeprecatedToolChecks.isDeprecatedWalker;
+
 /**
  * A GenomeAnalysisEngine that runs a specified walker.
  */
@@ -288,40 +291,6 @@ public class GenomeAnalysisEngine {
         //return result;
     }
 
-    // TODO -- Let's move this to a utility class in unstable - but which one?
-    // **************************************************************************************
-    // *                            Handle Deprecated Walkers                               *
-    // **************************************************************************************
-
-    // Mapping from walker name to major version number where the walker first disappeared
-    private static Map<String, String> deprecatedGATKWalkers = new HashMap<String, String>();
-    static {
-        deprecatedGATKWalkers.put("CountCovariates", "2.0");
-        deprecatedGATKWalkers.put("TableRecalibration", "2.0");
-        deprecatedGATKWalkers.put("AlignmentWalker", "2.2");
-        deprecatedGATKWalkers.put("CountBestAlignments", "2.2");
-    }
-
-    /**
-     * Utility method to check whether a given walker has been deprecated in a previous GATK release
-     *
-     * @param walkerName   the walker class name (not the full package) to check
-     */
-    public static boolean isDeprecatedWalker(final String walkerName) {
-        return deprecatedGATKWalkers.containsKey(walkerName);
-    }
-
-    /**
-     * Utility method to check whether a given walker has been deprecated in a previous GATK release
-     *
-     * @param walkerName   the walker class name (not the full package) to check
-     */
-    public static String getDeprecatedMajorVersionNumber(final String walkerName) {
-        return deprecatedGATKWalkers.get(walkerName);
-    }
-
-    // **************************************************************************************
-
     /**
      * Retrieves an instance of the walker based on the walker name.
      *
@@ -333,7 +302,7 @@ public class GenomeAnalysisEngine {
             return walkerManager.createByName(walkerName);
         } catch ( UserException e ) {
             if ( isDeprecatedWalker(walkerName) ) {
-                e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName));
+                e = new UserException.DeprecatedWalker(walkerName, getWalkerDeprecationInfo(walkerName));
             }
             throw e;
         }
@@ -565,6 +534,8 @@ public class GenomeAnalysisEngine {
         if ( intervals != null && intervals.isEmpty() ) {
             logger.warn("The given combination of -L and -XL options results in an empty set.  No intervals to process.");
         }
+
+        // TODO: add a check for ActiveRegion walkers to prevent users from passing an entire contig/chromosome
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -44,6 +44,7 @@ import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import it.unimi.dsi.fastutil.objects.ObjectOpenHashSet;
 
 import java.util.*;
 
@@ -155,7 +156,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
      * If multiple records in the rod overlap the given position, one is chosen arbitrarily.
      */
     @Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls; see documentation for more details", required=false)
-    protected List<String> expressionsToUse = new ArrayList<String>();
+    protected Set<String> expressionsToUse = new ObjectOpenHashSet();
 
     /**
      * Note that the -XL argument can be used along with this one to exclude annotations.
@@ -189,9 +190,10 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
      */
     public void initialize() {
 
-        if ( LIST )
+        if ( LIST ) {
             HelpUtils.listAnnotations();
             System.exit(0);
+        }
 
         // get the list of all sample names from the variant VCF input rod, if applicable
         List<String> rodName = Arrays.asList(variantCollection.variants.getName());

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -104,7 +104,7 @@ public class VariantAnnotatorEngine {
     }
 
     // select specific expressions to use
-    public void initializeExpressions(List<String> expressionsToUse) {
+    public void initializeExpressions(Set<String> expressionsToUse) {
         // set up the expressions
         for ( String expression : expressionsToUse )
             requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
+import org.broadinstitute.sting.utils.DeprecatedToolChecks;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -58,7 +59,7 @@ public class AnnotationInterfaceManager {
                 if ( interfaceClass == null )
                     interfaceClass = classMap.get(group + "Annotation");
                 if ( interfaceClass == null )
-                    throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly");
+                    throw new UserException.BadArgumentValue("group", "Annotation group " + group + " was not found; please check that you have specified the group name correctly");
             }
         }
 
@@ -67,8 +68,13 @@ public class AnnotationInterfaceManager {
             Class annotationClass = classMap.get(annotation);
             if ( annotationClass == null )
                 annotationClass = classMap.get(annotation + "Annotation");
-            if ( annotationClass == null )
+            if ( annotationClass == null ) {
-                throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly");
+                if (DeprecatedToolChecks.isDeprecatedAnnotation(annotation) ) {
+                    throw new UserException.DeprecatedAnnotation(annotation, DeprecatedToolChecks.getAnnotationDeprecationInfo(annotation));
+                } else {
+                    throw new UserException.BadArgumentValue("annotation", "Annotation " + annotation + " was not found; please check that you have specified the annotation name correctly");
+                }
+            }
         }
     }
 

public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java

@@ -0,0 +1,95 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.utils;
+
+import it.unimi.dsi.fastutil.objects.Object2ObjectMap;
+import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
+
+import java.util.*;
+
+/**
+ * Utility class for handling deprecated tools gracefully
+ *
+ * @author vdauwera
+ * @since 3/11/13
+ */
+public class DeprecatedToolChecks {
+
+    // Mapping from walker name to major version number where the walker first disappeared and optional replacement options
+    private static Object2ObjectMap deprecatedGATKWalkers = new Object2ObjectOpenHashMap();
+    static {
+        // Indicate recommended replacement in parentheses if applicable
+        deprecatedGATKWalkers.put("CountCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("AnalyzeCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
+        deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");
+    }
+
+    // Mapping from walker name to major version number where the walker first disappeared and optional replacement options
+    private static Object2ObjectMap deprecatedGATKAnnotations = new Object2ObjectOpenHashMap();
+    static {
+        // Same comments as for walkers
+        deprecatedGATKAnnotations.put("DepthOfCoverage", "2.4 (renamed to Coverage)");
+    }
+
+    /**
+     * Utility method to check whether a given walker has been deprecated in a previous GATK release
+     *
+     * @param walkerName   the walker class name (not the full package) to check
+     */
+    public static boolean isDeprecatedWalker(final String walkerName) {
+        return deprecatedGATKWalkers.containsKey(walkerName);
+    }
+
+    /**
+     * Utility method to check whether a given annotation has been deprecated in a previous GATK release
+     *
+     * @param annotationName   the annotation class name (not the full package) to check
+     */
+    public static boolean isDeprecatedAnnotation(final String annotationName) {
+        return deprecatedGATKAnnotations.containsKey(annotationName);
+    }
+
+    /**
+     * Utility method to pull up the version number at which a walker was deprecated and the suggested replacement, if any
+     *
+     * @param walkerName   the walker class name (not the full package) to check
+     */
+    public static String getWalkerDeprecationInfo(final String walkerName) {
+        return deprecatedGATKWalkers.get(walkerName).toString();
+    }
+
+    /**
+     * Utility method to pull up the version number at which an annotation was deprecated and the suggested replacement, if any
+     *
+     * @param annotationName   the annotation class name (not the full package) to check
+     */
+    public static String getAnnotationDeprecationInfo(final String annotationName) {
+        return deprecatedGATKAnnotations.get(annotationName).toString();
+    }
+
+}

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

@@ -371,14 +371,18 @@ public class UserException extends ReviewedStingException {
         }
     }
 
-
-
     public static class DeprecatedWalker extends UserException {
         public DeprecatedWalker(String walkerName, String version) {
             super(String.format("Walker %s is no longer available in the GATK; it has been deprecated since version %s", walkerName, version));
         }
     }
 
+    public static class DeprecatedAnnotation extends UserException {
+        public DeprecatedAnnotation(String annotationName, String version) {
+            super(String.format("Annotation %s is no longer available in the GATK; it has been deprecated since version %s", annotationName, version));
+        }
+    }
+
     public static class CannotExecuteQScript extends UserException {
         public CannotExecuteQScript(String message) {
             super(String.format("Unable to execute QScript: " + message));