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GenotypeAnnotations now accept a GenotypeBuilder and directly update the builder with their value 

-- Cleans up interface and avoids significant amounts of gross typing code
This commit is contained in:
Mark DePristo 2012-06-11 13:57:48 -04:00
parent 7506994d09
commit 9ac4203254
5 changed files with 37 additions and 44 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -11,6 +11,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
@ -21,15 +22,12 @@ import java.util.*;
*/
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) {
Double ratio = annotateSNP(stratifiedContext, vc, g);
if (ratio == null)
return null;
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", ratio.doubleValue()));
return map;
return;
gb.attribute(getKeyNames().get(0), Double.valueOf(String.format("%.2f", ratio.doubleValue())));
}
private Double annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {

32
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -15,6 +15,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
@ -45,22 +46,20 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) {
if ( g == null || !g.isCalled() )
return null;
return;
if ( vc.isSNP() )
return annotateSNP(stratifiedContext, vc);
if ( vc.isIndel() )
return annotateIndel(stratifiedContext, vc);
return null;
annotateSNP(stratifiedContext, vc, gb);
else if ( vc.isIndel() )
annotateIndel(stratifiedContext, vc, gb);
}
private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
private void annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, GenotypeBuilder gb) {
if ( ! stratifiedContext.hasBasePileup() )
return null;
return;
HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
for ( Allele allele : vc.getAlleles() )
@ -78,17 +77,16 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
counts[i+1] = alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]);
return toADAnnotation(counts);
gb.AD(counts);
}
private Map<String,Object> annotateIndel(AlignmentContext stratifiedContext, VariantContext vc) {
private void annotateIndel(AlignmentContext stratifiedContext, VariantContext vc, GenotypeBuilder gb) {
if ( ! stratifiedContext.hasBasePileup() )
return null;
return;
ReadBackedPileup pileup = stratifiedContext.getBasePileup();
if ( pileup == null )
return null;
return;
final HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();
alleleCounts.put(REF_ALLELE, 0);
@ -129,11 +127,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
counts[i+1] = alleleCounts.get( getAlleleRepresentation(vc.getAlternateAllele(i)) );
return toADAnnotation(counts);
}
private final Map<String, Object> toADAnnotation(final int[] counts) {
return Collections.singletonMap(getKeyNames().get(0), (Object)counts);
gb.AD(counts);
}
private String getAlleleRepresentation(Allele allele) {

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
@ -47,10 +48,11 @@ import java.util.Map;
* Count for each sample of mapping quality zero reads
*/
public class MappingQualityZeroBySample extends GenotypeAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker,
AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g) {
public void annotate(RefMetaDataTracker tracker,
AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context,
VariantContext vc, Genotype g, GenotypeBuilder gb) {
if ( g == null || !g.isCalled() )
return null;
return;
int mq0 = 0;
if ( context.hasBasePileup() ) {
@ -60,9 +62,8 @@ public class MappingQualityZeroBySample extends GenotypeAnnotation {
mq0++;
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%d", mq0));
return map;
gb.attribute(getKeyNames().get(0), mq0);
}
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }

20
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -261,24 +261,22 @@ public class VariantAnnotatorEngine {
}
private GenotypesContext annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( requestedGenotypeAnnotations.size() == 0 )
if ( requestedGenotypeAnnotations.isEmpty() )
return vc.getGenotypes();
GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
for ( final Genotype genotype : vc.getGenotypes() ) {
AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
if ( context == null ) {
genotypes.add(genotype);
continue;
} else {
final GenotypeBuilder gb = new GenotypeBuilder(genotype);
for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
annotation.annotate(tracker, walker, ref, context, vc, genotype, gb);
}
genotypes.add(gb.make());
}
Map<String, Object> genotypeAnnotations = new HashMap<String, Object>(genotype.getExtendedAttributes());
for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
Map<String, Object> result = annotation.annotate(tracker, walker, ref, context, vc, genotype);
if ( result != null )
genotypeAnnotations.putAll(result);
}
genotypes.add(new GenotypeBuilder(genotype).attributes(genotypeAnnotations).make());
}
return genotypes;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
@ -13,8 +14,9 @@ import java.util.Map;
public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts/genotype split by sample
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker,
ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker,
ReferenceContext ref, AlignmentContext stratifiedContext,
VariantContext vc, Genotype g, GenotypeBuilder gb );
// return the descriptions used for the VCF FORMAT meta field
public abstract List<VCFFormatHeaderLine> getDescriptions();