Item #3 -- "Address my maintenance concerns about

AnnotationUtils.isAlleleSpecific()"

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java

@@ -50,16 +50,7 @@ public static String encodeAnyASList( final List<?> somethingList) {
      * @return true if the annotation is expected to have values per-allele
      */
     public static boolean isAlleleSpecific(final InfoFieldAnnotation annotation) {
-        if (annotation instanceof AS_RankSumTest) {
-            return true;
-        }
-        if (annotation instanceof AS_StrandBiasTest) {
-            return true;
-        }
-        if (annotation instanceof AS_RMSMappingQuality) {
-            return true;
-        }
-        if (annotation instanceof AS_StandardAnnotation) {
+        if (annotation instanceof AlleleSpecificAnnotation) {
             return true;
         }
         return false;

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_InbreedingCoeff.java

@@ -40,7 +40,7 @@
  */
 //TODO: this can't extend InbreedingCoeff because that one is Standard and it would force this to be output all the time; should fix code duplication nonetheless
 @DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Allele-specific likelihood-based test for the consanguinity among samples (AS_InbreedingCoeff)")
-public final class AS_InbreedingCoeff extends InfoFieldAnnotation implements AS_StandardAnnotation {
+public final class AS_InbreedingCoeff extends InfoFieldAnnotation implements AS_StandardAnnotation, AlleleSpecificAnnotation {
 
     public static final int MIN_SAMPLES = 10;
     private Set<String> founderIds;    //TODO: either use this or enter a bug report

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java

@@ -46,7 +46,7 @@
  * </ul>
  */
 @DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Allele-specific call confidence normalized by depth of sample reads supporting the allele (AS_QD)")
-public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnnotation, AS_StandardAnnotation {
+public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnnotation, AS_StandardAnnotation, AlleleSpecificAnnotation {
 
     @Override
     public List<String> getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY); }

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java

@@ -43,7 +43,7 @@
  * </ul>
  */
 @DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Allele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ)")
-public final class AS_RMSMappingQuality extends InfoFieldAnnotation implements AS_StandardAnnotation, ReducibleAnnotation {
+public final class AS_RMSMappingQuality extends InfoFieldAnnotation implements AS_StandardAnnotation, ReducibleAnnotation, AlleleSpecificAnnotation {
 
     private final String printFormat = "%.2f";
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java

@@ -21,7 +21,7 @@
 /**
  * Allele-specific implementation of rank sum test annotations
  */
-public abstract class AS_RankSumTest extends RankSumTest implements ReducibleAnnotation {
+public abstract class AS_RankSumTest extends RankSumTest implements ReducibleAnnotation, AlleleSpecificAnnotation {
     private static final Logger logger = LogManager.getLogger(AS_RankSumTest.class);
     public static final String RAW_DELIM = ",";
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_StrandBiasTest.java

@@ -18,7 +18,7 @@
 /**
  * Allele-specific implementation of strand bias annotations
  */
-public abstract class AS_StrandBiasTest extends StrandBiasTest implements ReducibleAnnotation {
+public abstract class AS_StrandBiasTest extends StrandBiasTest implements ReducibleAnnotation, AlleleSpecificAnnotation {
     private final static Logger logger = LogManager.getLogger(AS_StrandBiasTest.class);
     public static final String SPLIT_DELIM = "\\|"; //String.split takes a regex, so we need to escape the pipe
     public static final String PRINT_DELIM = "|";