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Next iteration of new VA interface: extend changes to per-genotype annotations as well. Will allow to have AD correctly implemented at last (that change not done yet)

This commit is contained in:
Guillermo del Angel 2012-08-20 12:52:15 -04:00
parent c384677917
commit 5b5fee56cf
5 changed files with 41 additions and 14 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -24,7 +25,14 @@ import java.util.List;
*/ */
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation { public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) { public void annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final AlignmentContext stratifiedContext,
final VariantContext vc,
final Genotype g,
final GenotypeBuilder gb,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
Double ratio = annotateSNP(stratifiedContext, vc, g); Double ratio = annotateSNP(stratifiedContext, vc, g);
if (ratio == null) if (ratio == null)
return; return;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
@ -48,7 +49,8 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
final AlignmentContext stratifiedContext, final AlignmentContext stratifiedContext,
final VariantContext vc, final VariantContext vc,
final Genotype g, final Genotype g,
final GenotypeBuilder gb) { final GenotypeBuilder gb,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
if ( g == null || !g.isCalled() ) if ( g == null || !g.isCalled() )
return; return;

14
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -46,14 +47,19 @@ import java.util.List;
* Count for each sample of mapping quality zero reads * Count for each sample of mapping quality zero reads
*/ */
public class MappingQualityZeroBySample extends GenotypeAnnotation { public class MappingQualityZeroBySample extends GenotypeAnnotation {
public void annotate(RefMetaDataTracker tracker, public void annotate(final RefMetaDataTracker tracker,
AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext context, final AnnotatorCompatible walker,
VariantContext vc, Genotype g, GenotypeBuilder gb) { final ReferenceContext ref,
final AlignmentContext stratifiedContext,
final VariantContext vc,
final Genotype g,
final GenotypeBuilder gb,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
if ( g == null || !g.isCalled() ) if ( g == null || !g.isCalled() )
return; return;
int mq0 = 0; int mq0 = 0;
final ReadBackedPileup pileup = context.getBasePileup(); final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
for (PileupElement p : pileup ) { for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 ) if ( p.getMappingQual() == 0 )
mq0++; mq0++;

15
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -210,7 +210,7 @@ public class VariantAnnotatorEngine {
VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations); VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations);
// annotate genotypes, creating another new VC in the process // annotate genotypes, creating another new VC in the process
return builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc)).make(); return builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap)).make();
} }
public VariantContext annotateContext(final Map<String, PerReadAlleleLikelihoodMap> stratifiedContexts, VariantContext vc) { public VariantContext annotateContext(final Map<String, PerReadAlleleLikelihoodMap> stratifiedContexts, VariantContext vc) {
@ -278,20 +278,25 @@ public class VariantAnnotatorEngine {
} }
} }
private GenotypesContext annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { private GenotypesContext annotateGenotypes(final RefMetaDataTracker tracker,
final ReferenceContext ref, final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String,PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( requestedGenotypeAnnotations.isEmpty() ) if ( requestedGenotypeAnnotations.isEmpty() )
return vc.getGenotypes(); return vc.getGenotypes();
final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples()); final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
for ( final Genotype genotype : vc.getGenotypes() ) { for ( final Genotype genotype : vc.getGenotypes() ) {
AlignmentContext context = stratifiedContexts.get(genotype.getSampleName()); final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());
if ( context == null ) { if ( context == null && perReadAlleleLikelihoodMap == null) {
// no likelihoods nor pileup available: just move on to next sample
genotypes.add(genotype); genotypes.add(genotype);
} else { } else {
final GenotypeBuilder gb = new GenotypeBuilder(genotype); final GenotypeBuilder gb = new GenotypeBuilder(genotype);
for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) { for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
annotation.annotate(tracker, walker, ref, context, vc, genotype, gb); annotation.annotate(tracker, walker, ref, context, vc, genotype, gb, perReadAlleleLikelihoodMap);
} }
genotypes.add(gb.make()); genotypes.add(gb.make());
} }

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
@ -13,9 +14,14 @@ import java.util.List;
public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation { public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts/genotype split by sample // return annotations for the given contexts/genotype split by sample
public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, public abstract void annotate(final RefMetaDataTracker tracker,
ReferenceContext ref, AlignmentContext stratifiedContext, final AnnotatorCompatible walker,
VariantContext vc, Genotype g, GenotypeBuilder gb ); final ReferenceContext ref,
final AlignmentContext stratifiedContext,
final VariantContext vc,
final Genotype g,
final GenotypeBuilder gb,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap);
// return the descriptions used for the VCF FORMAT meta field // return the descriptions used for the VCF FORMAT meta field
public abstract List<VCFFormatHeaderLine> getDescriptions(); public abstract List<VCFFormatHeaderLine> getDescriptions();