RefMetaDataTracker no longer automagically converts inputs to VariantContexts

This was no longer working properly given that DBSNP indels needed to be moved around.  The adaptor system is being refactored and you will need to convert files from X -> VCF for many tools to work.

public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java

@@ -54,37 +54,12 @@ public class RefMetaDataTracker {
         else {
             map = new HashMap<String, RODRecordList>(allBindings.size());
             for ( RODRecordList rod : allBindings ) {
-                //logger.debug(String.format("Binding %s to %s", name, rod));
                 if ( rod != null )
-                    map.put(canonicalName(rod.getName()), maybeConvertToVariantContext(rod));
+                    map.put(canonicalName(rod.getName()), rod);
             }
         }
     }
 
-    /**
-     * A private converter that transforms a RODRecordList of objects of type X into
-     * a list of VariantContexts, if possible.
-     *
-     * TODO: should be removed when Features like dbsnp and hapmap produce VCs directly
-     *
-     * @param bindings
-     * @return
-     */
-    private final RODRecordList maybeConvertToVariantContext(RODRecordList bindings) {
-        List<GATKFeature> values = new ArrayList<GATKFeature>(bindings.size());
-
-        for ( GATKFeature rec : bindings ) {
-            if ( VariantContextAdaptors.canBeConvertedToVariantContext(rec.getUnderlyingObject()) ) {
-                final VariantContext vc = VariantContextAdaptors.toVariantContext(bindings.getName(), rec.getUnderlyingObject(), ref);
-                if ( vc != null ) // it's possible that the conversion failed, but we continue along anyway
-                    values.add(new GATKFeature.TribbleGATKFeature(ref.getGenomeLocParser(), vc, rec.getName()));
-            } else
-                values.add(rec);
-        }
-
-        return new RODRecordListImpl(bindings.getName(), values, bindings.getLocation());
-    }
-
     // ------------------------------------------------------------------------------------------
     //
     //