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New VariantAnnotatorEngine capability: an initialize() method for all annotation classes. 

All VariantAnnotator annotation classes may now have an (optional) initialize() method
that gets called by the VariantAnnotatorEngine ONCE before annotation starts.

As an example of how this can be used, the SnpEff annotation class will use the initialize()
method to check whether the SnpEff version number stored in the vcf header is a supported
version, and also to verify that its required RodBinding is present.
This commit is contained in:
David Roazen 2011-09-12 12:28:23 -04:00
parent 981b78ea50
commit 9d9d438bc4
5 changed files with 19 additions and 10 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -86,6 +86,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
public RodBinding<VariantContext> getVariantRodBinding() { return variantCollection.variants; }
/**
* The INFO field will be annotated with information on the most biologically-significant effect
@ -208,6 +209,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, this);
engine.initializeExpressions(expressionsToUse);
engine.invokeAnnotationInitializationMethods();
// setup the header fields
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();

15
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -29,10 +29,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
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.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
@ -113,6 +110,16 @@ public class VariantAnnotatorEngine {
dbAnnotations.put(rod, rod.getName());
}
public void invokeAnnotationInitializationMethods() {
for ( VariantAnnotatorAnnotation annotation : requestedInfoAnnotations ) {
annotation.initialize(walker);
}
for ( VariantAnnotatorAnnotation annotation : requestedGenotypeAnnotations ) {
annotation.initialize(walker);
}
}
public Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
Set<VCFHeaderLine> descriptions = new HashSet<VCFHeaderLine>();

1
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
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@ -9,6 +9,7 @@ import java.util.List;
public interface AnnotatorCompatibleWalker {
// getter methods for various used bindings
public abstract RodBinding<VariantContext> getVariantRodBinding();
public abstract RodBinding<SnpEffFeature> getSnpEffRodBinding();
public abstract RodBinding<VariantContext> getDbsnpRodBinding();
public abstract List<RodBinding<VariantContext>> getCompRodBindings();

9
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
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@ -24,18 +24,15 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
public abstract class VariantAnnotatorAnnotation {
// return the INFO keys
public abstract List<String> getKeyNames();
// initialization method (optional for subclasses, and therefore non-abstract)
public void initialize ( AnnotatorCompatibleWalker walker ) { }
}

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -127,6 +127,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
@ArgumentCollection
protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
public RodBinding<VariantContext> getVariantRodBinding() { return null; }
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }