Make several Funcotator methods and fields protected so it is easiest…

… to extend the tool (#8166)
broadinstitute · Feb 1, 2023 · d1a4f94 · d1a4f94
1 parent a3c1d2c
commit d1a4f94
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
@@ -121,7 +121,7 @@ public FuncotatorEngine(final BaseFuncotatorArgumentCollection funcotatorArgs,
     /**
      * @return An unmodifiable {@link List<DataSourceFuncotationFactory>} being used by this {@link FuncotatorEngine} to create {@link Funcotation}s.
      */
-    List<DataSourceFuncotationFactory> getFuncotationFactories() {
+    public List<DataSourceFuncotationFactory> getFuncotationFactories() {
         return Collections.unmodifiableList(dataSourceFactories);
     }
 
@@ -427,7 +427,7 @@ public boolean onlyProducedIGRs() {
      * @param annotationMap {@link Map} (of ANNOTATION_NAME : ANNOTATION_VALUE) to check
      * @return A {@link LinkedHashMap} of annotations in the given {@code annotationMap} that do not occur in the given {@code dataSourceFactories}.
      */
-    private LinkedHashMap<String, String> getUnaccountedForAnnotations( final List<DataSourceFuncotationFactory> dataSourceFactories,
+    public LinkedHashMap<String, String> getUnaccountedForAnnotations( final List<DataSourceFuncotationFactory> dataSourceFactories,
                                                                         final Map<String, String> annotationMap ) {
         final LinkedHashMap<String, String> outAnnotations = new LinkedHashMap<>();