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Implemented SB for UGv2. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4477 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-11 03:56:01 +00:00
parent 7008a469dc
commit f28523e7de
1 changed files with 53 additions and 14 deletions
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67
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -197,6 +197,10 @@ public class UnifiedGenotyperEngine {
for ( Genotype g : genotypes.values() ) for ( Genotype g : genotypes.values() )
alleles.addAll(g.getAlleles()); alleles.addAll(g.getAlleles());
// print out stats if we have a writer
if ( verboseWriter != null )
printVerboseData(refContext.getLocus().toString(), alleles, PofF, phredScaledConfidence, normalizedPosteriors);
// *** note that calculating strand bias involves overwriting data structures, so we do that last // *** note that calculating strand bias involves overwriting data structures, so we do that last
HashMap<String, Object> attributes = new HashMap<String, Object>(); HashMap<String, Object> attributes = new HashMap<String, Object>();
@ -211,16 +215,44 @@ public class UnifiedGenotyperEngine {
if ( !UAC.NO_SLOD ) { if ( !UAC.NO_SLOD ) {
// TODO: implement me // the overall lod
double overallLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
//Map<String, BiallelicGenotypeLikelihoods> forwardGLs = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.FORWARD, genotypePriors); double overallLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess];
//Map<String, BiallelicGenotypeLikelihoods> reverseGLs = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.REVERSE, genotypePriors); double lod = overallLog10PofF - overallLog10PofNull;
//System.out.println("overallLog10PofNull=" + overallLog10PofNull + ", overallLog10PofF=" + overallLog10PofF);
// set the optimization value for the subsequent strand calculations
afcm.get().setMinAlleleFrequencyToTest(bestAFguess);
// the forward lod
GLs.clear();
glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.FORWARD, genotypePriors, GLs);
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get());
double forwardLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
double forwardLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess];
//System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF);
// the reverse lod
GLs.clear();
glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.REVERSE, genotypePriors, GLs);
clearAFarray(log10AlleleFrequencyPosteriors.get());
afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get());
double reverseLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
double reverseLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess];
//System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ", reverseLog10PofF=" + reverseLog10PofF);
double forwardLod = forwardLog10PofF + reverseLog10PofNull - overallLog10PofNull;
double reverseLod = reverseLog10PofF + forwardLog10PofNull - overallLog10PofNull;
//System.out.println("forward lod=" + forwardLod + ", reverse lod=" + reverseLod);
// strand score is max bias between forward and reverse strands
double strandScore = Math.max(forwardLod - lod, reverseLod - lod);
// rescale by a factor of 10
strandScore *= 10.0;
//logger.debug(String.format("SLOD=%f", strandScore));
attributes.put("SB", Double.valueOf(strandScore));
} }
GenomeLoc loc = refContext.getLocus(); GenomeLoc loc = refContext.getLocus();
@ -246,10 +278,6 @@ public class UnifiedGenotyperEngine {
vc = variantContexts.iterator().next(); //We know the collection will always have exactly 1 element. vc = variantContexts.iterator().next(); //We know the collection will always have exactly 1 element.
} }
// print out stats if we have a writer
if ( verboseWriter != null )
printVerboseData(vc, PofF, phredScaledConfidence, normalizedPosteriors);
VariantCallContext call = new VariantCallContext(vc, passesCallThreshold(phredScaledConfidence, atTriggerTrack)); VariantCallContext call = new VariantCallContext(vc, passesCallThreshold(phredScaledConfidence, atTriggerTrack));
call.setRefBase(refContext.getBase()); call.setRefBase(refContext.getBase());
return call; return call;
@ -338,15 +366,26 @@ public class UnifiedGenotyperEngine {
return new VariantCallContext(QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING); return new VariantCallContext(QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING);
} }
protected void printVerboseData(VariantContext vc, double PofF, double phredScaledConfidence, double[] normalizedPosteriors) { protected void printVerboseData(String pos, Set<Allele> alleles, double PofF, double phredScaledConfidence, double[] normalizedPosteriors) {
Allele refAllele = null, altAllele = null;
for ( Allele allele : alleles ) {
if ( allele.isReference() )
refAllele = allele;
else
altAllele = allele;
}
for (int i = 0; i <= N; i++) { for (int i = 0; i <= N; i++) {
StringBuilder AFline = new StringBuilder("AFINFO\t"); StringBuilder AFline = new StringBuilder("AFINFO\t");
AFline.append(vc.getChr()).append(":").append(vc.getStart()).append("\t"); AFline.append(pos);
AFline.append(vc.getReference()).append("\t"); AFline.append("\t");
if ( vc.isBiallelic() ) AFline.append(refAllele);
AFline.append(vc.getAlternateAllele(0)).append("\t"); AFline.append("\t");
if ( altAllele != null )
AFline.append(altAllele);
else else
AFline.append("N/A\t"); AFline.append("N/A");
AFline.append("\t");
AFline.append(i + "/" + N + "\t"); AFline.append(i + "/" + N + "\t");
AFline.append(String.format("%.2f\t", ((float)i)/N)); AFline.append(String.format("%.2f\t", ((float)i)/N));
AFline.append(String.format("%.8f\t", log10AlleleFrequencyPriors[i])); AFline.append(String.format("%.8f\t", log10AlleleFrequencyPriors[i]));