After dicussion with Ryan/Eric, the Structural_Indel variant type is now gone, and has been entirely replaced with the access pattern .isStructuralIndel(). This makes it a strict subtype of indel. I agree that this method is a bit more sensible.

In addition, fix for GSA-310. If supplied -rf argument does not match a known read filter, the list of read filters will be printed, and users directed to the documentation for more information.

public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java

@@ -25,9 +25,13 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
+import com.google.common.base.Function;
+import com.google.common.collect.Collections2;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 
 import java.util.Collection;
+import java.util.List;
 
 /**
  * Manage filters and filter options.  Any requests for basic filtering classes
@@ -54,4 +58,26 @@ public class FilterManager extends PluginManager<ReadFilter> {
     public Collection<Class<? extends ReadFilter>> getValues() {
         return this.getPlugins();
     }
+
+    /**
+     * Rather than use the default error message, print out a list of read filters as well.
+     * @param pluginCategory - string, the category of the plugin (e.g. read filter)
+     * @param pluginName - string, what we were trying to match (but failed to)
+     * @return - A wall of text with the default message, followed by a listing of available read filters
+     */
+    @Override
+    protected String formatErrorMessage(String pluginCategory, String pluginName) {
+        List<Class<? extends ReadFilter>> availableFilters = this.getPluginsImplementing(ReadFilter.class);
+        Collection<String> availableFilterNames = Collections2.transform(availableFilters, new Function<Class<? extends ReadFilter>,String>(){
+
+            @Override
+            public String apply(final Class<? extends ReadFilter> input) {
+                return getName(input);
+            }
+        });
+
+        return String.format("Read filter %s not found. Available read filters:%n%s.%n%n%s",pluginName,
+                Utils.join(String.format(", "),availableFilterNames),
+                "Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -286,7 +286,6 @@ public class VariantDataManager {
             case INDEL:
             case MIXED:
             case SYMBOLIC:
-            case STRUCTURAL_INDEL:
                 return checkVariationClass( evalVC, VariantRecalibratorArgumentCollection.Mode.INDEL );
             default:
                 return false;

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

@@ -277,7 +277,7 @@ public class PluginManager<PluginType> {
     public PluginType createByName(String pluginName) {
         Class<? extends PluginType> plugin = pluginsByName.get(pluginName);
         if( plugin == null )
-            throw new UserException(String.format("Could not find %s with name: %s", pluginCategory,pluginName));
+            throw new UserException(formatErrorMessage(pluginCategory,pluginName));
         try {
             return plugin.newInstance();
         } catch (Exception e) {
@@ -330,4 +330,14 @@ public class PluginManager<PluginType> {
 
         return pluginName;
     }
+
+    /**
+     * Generate the error message for the plugin manager. The message is allowed to depend on the class.
+     * @param pluginCategory - string, the category of the plugin (e.g. read filter)
+     * @param pluginName - string, what we were trying to match (but failed to)
+     * @return error message text describing the error
+     */
+    protected String formatErrorMessage(String pluginCategory, String pluginName ) {
+        return String.format("Could not find %s with name: %s", pluginCategory,pluginName);
+    }
 }

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -457,7 +457,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
         SNP,
         MNP,    // a multi-nucleotide polymorphism
         INDEL,
-        STRUCTURAL_INDEL,
         SYMBOLIC,
         MIXED,
     }
@@ -531,7 +530,17 @@ public class VariantContext implements Feature { // to enable tribble integratio
     }
 
     public boolean isStructuralIndel() {
-        return getType() == Type.STRUCTURAL_INDEL;
+        if ( getType() == Type.INDEL ) {
+            List<Integer> sizes = getIndelLengths();
+            if ( sizes != null ) {
+                for ( Integer length : sizes ) {
+                    if ( length > MAX_ALLELE_SIZE_FOR_NON_SV ) {
+                        return true;
+                    }
+                }
+            }
+        }
+        return false;
     }
 
     /**
@@ -716,7 +725,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
      * @return a list of indel lengths ( null if not of type indel or mixed )
      */
     public List<Integer> getIndelLengths() {
-        if ( getType() != Type.INDEL && getType() != Type.MIXED && getType() != Type.STRUCTURAL_INDEL ) {
+        if ( getType() != Type.INDEL && getType() != Type.MIXED ) {
             return null;
         }
 
@@ -1263,13 +1272,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
         // is reserved for cases of multiple alternate alleles of different types).  Therefore, if we've reached this point
         // in the code (so we're not a SNP, MNP, or symbolic allele), we absolutely must be an INDEL.
 
-        // Because a number of structural variation callers write the whole alternate allele into the VCF where possible,
-        // this can result in insertion/deletion alleles of structural variant size, e.g. 151+. As of July 2012, we now
-        // classify these as structural events, rather than indel events, as we think differently about the mechanism,
-        // representation, and handling of these events. Check for this case here:
-        if ( ref.length() > MAX_ALLELE_SIZE_FOR_NON_SV || allele.length() > MAX_ALLELE_SIZE_FOR_NON_SV )
-            return Type.STRUCTURAL_INDEL;
-
         return Type.INDEL;
 
         // old incorrect logic: