Replace string literals for annotation groups. Closes #1216.

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java

@@ -1066,7 +1066,7 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
      * Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
      */
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    //protected String[] annotationGroupsToUse = { "Standard" };
+    //protected String[] annotationGroupsToUse = { StandardAnnotation.class.getSimpleName() };
     protected String[] annotationClassesToUse = { };
 
     /**

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java

@@ -62,6 +62,8 @@ import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.gatk.engine.io.DirectOutputTracker;
 import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardHCAnnotation;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
@@ -328,7 +330,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
      */
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{ "Standard", "StandardHCAnnotation" }));
+    protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{StandardAnnotation.class.getSimpleName(), StandardHCAnnotation.class.getSimpleName() }));
 
     @ArgumentCollection
     private HaplotypeCallerArgumentCollection HCAC = new HaplotypeCallerArgumentCollection();

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java

@@ -54,6 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.variantutils;
 import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
@@ -129,7 +130,7 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
      * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
      */
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    protected String[] annotationGroupsToUse = { "Standard" };
+    protected String[] annotationGroupsToUse = { StandardAnnotation.class.getSimpleName() };
 
 
     /**

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java

@@ -65,7 +65,9 @@ import org.broadinstitute.gatk.engine.walkers.RodWalker;
 import org.broadinstitute.gatk.engine.walkers.TreeReducible;
 import org.broadinstitute.gatk.engine.walkers.Window;
 import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedArgumentCollection;
 import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine;
 import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyFailOverAFCalculatorProvider;
@@ -169,7 +171,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
      * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
      */
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{"Standard"}));
+    protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{StandardAnnotation.class.getSimpleName()}));
 
 
     /**
@@ -222,9 +224,13 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         annotationEngine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, Collections.<String>emptyList(), this, toolkit);
 
         // create the genotyping engine
-        boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY) || annotationGroupsToUse.contains("AS_Standard");
+        // when checking for presence of AS_StandardAnnotation we must deal with annoying feature that
-                genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger),
+        // the class name with or without the trailing "Annotation" are both valid command lines
-                toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping);
+        boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY)
+                || annotationGroupsToUse.contains(AS_StandardAnnotation.class.getSimpleName())
+                || annotationGroupsToUse.contains(AS_StandardAnnotation.class.getSimpleName().replace("Annotation", ""));
+        genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(),
+                GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger), toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping);
 
         // take care of the VCF headers
         final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);