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Initial implementation of annotator to compute allele balance for each sample 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4005 348d0f76-0448-11de-a6fe-93d51630548a
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flannick 2010-08-10 19:40:17 +00:00
parent 1dc373b9d0
commit 18fc5c8c3e
1 changed files with 68 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java 100755
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package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.vcf.VCFFormatHeaderLine;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broad.tribble.util.variantcontext.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.*;
import java.util.*;
public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, StratifiedAlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
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;
}
private Double annotateSNP(StratifiedAlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
double ratio = -1;
if ( !vc.isSNP() )
return null;
if ( !vc.isBiallelic() )
return null;
if ( g == null || !g.isCalled() )
return null;
if (!g.isHet())
return null;
Set<Allele> altAlleles = vc.getAlternateAlleles();
if ( altAlleles.size() == 0 )
return null;
final String bases = new String(stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases());
if ( bases.length() == 0 )
return null;
char refChr = vc.getReference().toString().charAt(0);
char altChr = vc.getAlternateAllele(0).toString().charAt(0);
int refCount = MathUtils.countOccurrences(refChr, bases);
int altCount = MathUtils.countOccurrences(altChr, bases);
// sanity check
if ( refCount + altCount == 0 )
return null;
ratio = ((double)refCount / (double)(refCount + altCount));
return ratio;
}
public List<String> getKeyNames() { return Arrays.asList("AB"); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), -1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
}