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QualByDepth was inefficiently iterating over the pileup 2 times for some reason. Removed non-useful annotation classes.

This commit is contained in:
Eric Banks 2011-11-02 12:58:38 -04:00
parent 4501dce58d
commit cf0e699226
3 changed files with 3 additions and 94 deletions
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32
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
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@ -1,32 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import java.util.Map;
/**
* Abstract base class for all annotations that are normalized by depth
*/
public abstract class AnnotationByDepth extends InfoFieldAnnotation {
protected int annotationByVariantDepth(final Map<String, Genotype> genotypes, Map<String, AlignmentContext> stratifiedContexts) {
int depth = 0;
for ( Map.Entry<String, Genotype> genotype : genotypes.entrySet() ) {
// we care only about variant calls
if ( genotype.getValue().isHomRef() )
continue;
AlignmentContext context = stratifiedContexts.get(genotype.getKey());
if ( context != null )
depth += context.size();
}
return depth;
}
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -4,6 +4,7 @@ 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.annotator.interfaces.AnnotatorCompatibleWalker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@ -20,7 +21,7 @@ import java.util.Map;
* *
* Low scores are indicative of false positive calls and artifacts. * Low scores are indicative of false positive calls and artifacts.
*/ */
public class QualByDepth extends AnnotationByDepth implements StandardAnnotation { public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 ) if ( stratifiedContexts.size() == 0 )
@ -48,8 +49,7 @@ public class QualByDepth extends AnnotationByDepth implements StandardAnnotation
if ( depth == 0 ) if ( depth == 0 )
return null; return null;
int qDepth = annotationByVariantDepth(genotypes, stratifiedContexts); double QD = 10.0 * vc.getNegLog10PError() / (double)depth;
double QD = 10.0 * vc.getNegLog10PError() / (double)qDepth;
Map<String, Object> map = new HashMap<String, Object>(); Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", QD)); map.put(getKeyNames().get(0), String.format("%.2f", QD));

59
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
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@ -1,59 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
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.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* SB annotation value by depth of alt containing samples
*/
public class SBByDepth extends AnnotationByDepth {
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;
if (!vc.hasAttribute(VCFConstants.STRAND_BIAS_KEY))
return null;
double sBias = vc.getAttributeAsDouble(VCFConstants.STRAND_BIAS_KEY, -1);
final Map<String, Genotype> genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() == 0 )
return null;
int sDepth = annotationByVariantDepth(genotypes, stratifiedContexts);
if ( sDepth == 0 )
return null;
double SbyD = (-sBias / (double)sDepth);
if (SbyD > 0)
SbyD = Math.log10(SbyD);
else
SbyD = -1000;
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", SbyD));
return map;
}
public List<String> getKeyNames() { return Arrays.asList("SBD"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Strand Bias by Depth")); }
}