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Mark Standard Annotations with an asterisk

This commit is contained in:
Eric Banks 2011-11-09 20:42:31 -05:00
parent 04b122be29
commit 82bf09edf3
1 changed files with 4 additions and 6 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -33,10 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
@ -180,15 +177,16 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
private void listAnnotationsAndExit() {
System.out.println("\nStandard annotations in the list below are marked with a '*'.");
List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
System.out.println("\nAvailable annotations for the VCF INFO field:");
for (int i = 0; i < infoAnnotationClasses.size(); i++)
System.out.println("\t" + infoAnnotationClasses.get(i).getSimpleName());
System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(infoAnnotationClasses.get(i)) ? "*" : "") + infoAnnotationClasses.get(i).getSimpleName());
System.out.println();
List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class).getPlugins();
System.out.println("\nAvailable annotations for the VCF FORMAT field:");
for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
System.out.println("\t" + genotypeAnnotationClasses.get(i).getSimpleName());
System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(genotypeAnnotationClasses.get(i)) ? "*" : "") + genotypeAnnotationClasses.get(i).getSimpleName());
System.out.println();
System.out.println("\nAvailable classes/groups of annotations:");
for ( Class c : new PluginManager<AnnotationType>(AnnotationType.class).getInterfaces() )