Addressing @droazen comments.

src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java

@@ -862,20 +862,6 @@ record = header.getProgramRecord(pgID);
         return pgID;
     }
 
-    /**
-     * Call {@link GATKTool#addFeatureInputsAfterInitialization(String, String, Class, int)} with no caching.
-     *
-     * @param filePath See {@link #addFeatureInputsAfterInitialization(String, String, Class, int)}
-     * @param name See {@link #addFeatureInputsAfterInitialization(String, String, Class, int)}
-     * @param featureType See {@link #addFeatureInputsAfterInitialization(String, String, Class, int)}
-     * @return The {@link FeatureInput} used as the key for this data source.
-     */
-    public FeatureInput<? extends Feature> addFeatureInputsAfterInitialization(final String filePath, final String name,
-                                                                               final Class<? extends Feature> featureType) {
-
-        return addFeatureInputsAfterInitialization(filePath, name, featureType, 0);
-    }
-
     /**
      * A method to allow a user to inject data sources after initialization that were not specified as command-line
      * arguments.
@@ -893,24 +879,6 @@ public FeatureInput<? extends Feature> addFeatureInputsAfterInitialization(final
 
         final FeatureInput<? extends Feature> featureInput = new FeatureInput<>(filePath, name);
 
-        //Add datasource to the feature manager too so that it can be queried. Setting lookahead to user's requested value.
-        addFeatureInputsAfterInitialization(featureInput, featureType, featureQueryLookahead);
-
-        return featureInput;
-    }
-
-    /**
-     * A method to allow a user to inject data sources after initialization that were not specified as command-line
-     * arguments.
-     *
-     * @param featureInput
-     * @param featureType class of feature in the feature input
-     * @param featureQueryLookahead look ahead this many bases during queries that produce cache misses
-     * @return The {@link FeatureInput} used as the key for this data source.
-     */
-    public void addFeatureInputsAfterInitialization(final FeatureInput<? extends Feature> featureInput,
-                                                    final Class<? extends Feature> featureType,
-                                                    final int featureQueryLookahead) {
         // Add datasource to the feature manager too so that it can be queried.
         // Setting lookahead to user-requested value:
         features.addToFeatureSources(
@@ -921,6 +889,8 @@ public void addFeatureInputsAfterInitialization(final FeatureInput<? extends Fea
                 cloudIndexPrefetchBuffer,
                 referenceArguments.getReferencePath()
         );
+
+        return featureInput;
     }
 
     /**

src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java

@@ -270,17 +270,25 @@ public void onTraversalStart() {
         funcotatorArgs.dataSourceDirectories.sort(Comparator.naturalOrder());
         final Map<Path, Properties> configData = DataSourceUtils.getAndValidateDataSourcesFromPaths(funcotatorArgs.referenceVersion, funcotatorArgs.dataSourceDirectories);
 
-        // Create the metadata directly from the input.
-        funcotatorEngine = new FuncotatorEngine(VcfFuncotationMetadata.create(new ArrayList<>(getHeaderForVariants().getInfoHeaderLines())),
-                DataSourceUtils.createDataSourceFuncotationFactoriesForDataSources(configData, annotationOverridesMap,
-                        funcotatorArgs.transcriptSelectionMode, finalUserTranscriptIdSet));
-
-        // Note that the next line has the effect of registering the FeatureInputs with the engine (via addFeatureInputsAfterInitialization).
-        //   If a funcotation factory feature input (i.e. the source file as a feature input) is null, then the funcotation
-        //   factory is not locatable.
-        funcotatorEngine.getFuncotationFactories().stream()
-                .filter(ff -> ff.getMainSourceFileAsFeatureInput() != null)
-                .forEach(ff -> addFeatureInputsAfterInitialization(ff.getMainSourceFileAsFeatureInput(), ff.getAnnotationFeatureClass(), funcotatorArgs.lookaheadFeatureCachingInBp));
+        // Create the data sources from the input:
+        // This will also create and register the FeatureInputs (created by the Data Sources)
+        // with the GATK Engine, so we do not have to plumb them in after the fact.
+        final List<DataSourceFuncotationFactory> dataSourceFuncotationFactories = DataSourceUtils.createDataSourceFuncotationFactoriesForDataSources(
+                configData,
+                annotationOverridesMap,
+                funcotatorArgs.transcriptSelectionMode,
+                finalUserTranscriptIdSet,
+                this,
+                funcotatorArgs.lookaheadFeatureCachingInBp
+        );
+
+        // Create our engine to do our work and drive this Funcotation train!
+        funcotatorEngine = new FuncotatorEngine(
+                VcfFuncotationMetadata.create(
+                    new ArrayList<>(getHeaderForVariants().getInfoHeaderLines())
+                ),
+                dataSourceFuncotationFactories
+        );
 
         // Determine which annotations are accounted for (by the funcotation factories) and which are not.
         final LinkedHashMap<String, String> unaccountedForDefaultAnnotations = getUnaccountedForAnnotations( funcotatorEngine.getFuncotationFactories(), annotationDefaultsMap );