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Give Annotations access to rod data. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2504 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-05 18:53:01 +00:00
parent 331d6db783
commit d8351cb9fc
13 changed files with 31 additions and 20 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.*; import org.broadinstitute.sting.utils.genotype.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@ -12,7 +13,7 @@ import java.util.Map;
public class AlleleBalance extends StandardVariantAnnotation { public class AlleleBalance extends StandardVariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( !(variation instanceof VariantBackedByGenotype) ) if ( !(variation instanceof VariantBackedByGenotype) )
return null; return null;

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord; import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@ -11,7 +12,7 @@ import java.util.Map;
public class DepthOfCoverage extends StandardVariantAnnotation { public class DepthOfCoverage extends StandardVariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
int depth = 0; int depth = 0;
for ( String sample : stratifiedContexts.keySet() ) for ( String sample : stratifiedContexts.keySet() )
depth += stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size(); depth += stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size();

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.*; import org.broadinstitute.sting.utils.genotype.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
@ -16,7 +17,7 @@ public class HardyWeinberg implements VariantAnnotation {
private static final int MIN_GENOTYPE_QUALITY = 10; private static final int MIN_GENOTYPE_QUALITY = 10;
private static final int MIN_NEG_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10; private static final int MIN_NEG_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10;
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( !(variation instanceof VariantBackedByGenotype) ) if ( !(variation instanceof VariantBackedByGenotype) )
return null; return null;

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@ -11,7 +12,7 @@ import java.util.Map;
public class HomopolymerRun extends StandardVariantAnnotation { public class HomopolymerRun extends StandardVariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( !variation.isBiallelic() || !variation.isSNP() ) if ( !variation.isBiallelic() || !variation.isSNP() )
return null; return null;

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
@ -12,7 +13,7 @@ import java.util.Map;
public class MappingQualityZero implements VariantAnnotation { public class MappingQualityZero implements VariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
int mq0 = 0; int mq0 = 0;
for ( String sample : stratifiedContexts.keySet() ) { for ( String sample : stratifiedContexts.keySet() ) {
ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(); ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype; import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.utils.genotype.Genotype; import org.broadinstitute.sting.utils.genotype.Genotype;
@ -15,7 +16,7 @@ import java.util.ArrayList;
public class QualByDepth extends StandardVariantAnnotation { public class QualByDepth extends StandardVariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( !(variation instanceof VariantBackedByGenotype) ) if ( !(variation instanceof VariantBackedByGenotype) )
return null; return null;
final List<Genotype> genotypes = ((VariantBackedByGenotype)variation).getGenotypes(); final List<Genotype> genotypes = ((VariantBackedByGenotype)variation).getGenotypes();

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
@ -15,7 +16,7 @@ import java.util.ArrayList;
public class RMSMappingQuality extends StandardVariantAnnotation { public class RMSMappingQuality extends StandardVariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
ArrayList<Integer> qualities = new ArrayList<Integer>(); ArrayList<Integer> qualities = new ArrayList<Integer>();
for ( String sample : stratifiedContexts.keySet() ) { for ( String sample : stratifiedContexts.keySet() ) {
ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(); ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
@ -17,7 +18,7 @@ public class RankSumTest implements VariantAnnotation {
private final static boolean DEBUG = false; private final static boolean DEBUG = false;
private static final double minPValue = 1e-10; private static final double minPValue = 1e-10;
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( !(variation instanceof VariantBackedByGenotype) ) if ( !(variation instanceof VariantBackedByGenotype) )
return null; return null;

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
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@ -8,6 +8,7 @@ import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import java.util.Map; import java.util.Map;
@ -29,7 +30,7 @@ public class SecondBaseSkew implements VariantAnnotation {
public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(KEY_NAME, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Chi-square Secondary Base Skew"); } public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(KEY_NAME, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Chi-square Secondary Base Skew"); }
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( !variation.isBiallelic() || !variation.isSNP() ) if ( !variation.isBiallelic() || !variation.isSNP() )
return null; return null;

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@ -11,7 +12,7 @@ import java.util.Map;
public class SpanningDeletions extends StandardVariantAnnotation { public class SpanningDeletions extends StandardVariantAnnotation {
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
int deletions = 0; int deletions = 0;
int depth = 0; int depth = 0;
for ( String sample : stratifiedContexts.keySet() ) { for ( String sample : stratifiedContexts.keySet() ) {

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@ -11,7 +12,7 @@ import java.util.Map;
public interface VariantAnnotation { public interface VariantAnnotation {
// return the annotation for the given variation and context split by sample (return null for no annotation) // return the annotation for the given variation and context split by sample (return null for no annotation)
public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation); public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation);
// return the INFO key // return the INFO key
public String getKeyName(); public String getKeyName();

14
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -168,7 +168,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
variant.isSNP() ) { variant.isSNP() ) {
Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup(), null, null); Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup(), null, null);
if ( stratifiedContexts != null ) if ( stratifiedContexts != null )
annotations = getAnnotations(ref, stratifiedContexts, variant, requestedAnnotations); annotations = getAnnotations(tracker, ref, stratifiedContexts, variant, requestedAnnotations);
} }
writeVCF(tracker, ref, context, variant, annotations); writeVCF(tracker, ref, context, variant, annotations);
@ -210,26 +210,26 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
} }
// option #1: don't specify annotations to be used: standard annotations are used by default // option #1: don't specify annotations to be used: standard annotations are used by default
public static Map<String, String> getAnnotations(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( standardAnnotations == null ) if ( standardAnnotations == null )
determineAllAnnotations(); determineAllAnnotations();
return getAnnotations(ref, stratifiedContexts, variation, standardAnnotations.values()); return getAnnotations(tracker, ref, stratifiedContexts, variation, standardAnnotations.values());
} }
// option #2: specify that all possible annotations be used // option #2: specify that all possible annotations be used
public static Map<String, String> getAllAnnotations(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) { public static Map<String, String> getAllAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
if ( allAnnotations == null ) if ( allAnnotations == null )
determineAllAnnotations(); determineAllAnnotations();
return getAnnotations(ref, stratifiedContexts, variation, allAnnotations.values()); return getAnnotations(tracker, ref, stratifiedContexts, variation, allAnnotations.values());
} }
// option #3: specify the exact annotations to be used // option #3: specify the exact annotations to be used
public static Map<String, String> getAnnotations(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation, Collection<VariantAnnotation> annotations) { public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation, Collection<VariantAnnotation> annotations) {
HashMap<String, String> results = new HashMap<String, String>(); HashMap<String, String> results = new HashMap<String, String>();
for ( VariantAnnotation annotator : annotations) { for ( VariantAnnotation annotator : annotations) {
String annot = annotator.annotate(ref, stratifiedContexts, variation); String annot = annotator.annotate(tracker, ref, stratifiedContexts, variation);
if ( annot != null ) { if ( annot != null ) {
results.put(annotator.getKeyName(), annot); results.put(annotator.getKeyName(), annot);
} }

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -257,9 +257,9 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
if ( call != null && call.first != null && call.first instanceof ArbitraryFieldsBacked ) { if ( call != null && call.first != null && call.first instanceof ArbitraryFieldsBacked ) {
Map<String, String> annotations; Map<String, String> annotations;
if ( UAC.ALL_ANNOTATIONS ) if ( UAC.ALL_ANNOTATIONS )
annotations = VariantAnnotator.getAllAnnotations(refContext, stratifiedContexts, call.first); annotations = VariantAnnotator.getAllAnnotations(tracker, refContext, stratifiedContexts, call.first);
else else
annotations = VariantAnnotator.getAnnotations(refContext, stratifiedContexts, call.first); annotations = VariantAnnotator.getAnnotations(tracker, refContext, stratifiedContexts, call.first);
((ArbitraryFieldsBacked)call.first).setFields(annotations); ((ArbitraryFieldsBacked)call.first).setFields(annotations);
} }