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Make several Funcotator methods and fields protected #8166

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Feb 1, 2023
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Make several Funcotator methods and fields protected #8166

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4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
}

Expand Down Expand Up @@ -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<>();

Expand Down