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Renaming for accuracy 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4519 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-18 18:11:07 +00:00
parent 0fe504b748
commit 524cb8257c
3 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
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@ -104,7 +104,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
double[] log10AlleleFrequencyPosteriors, double[] log10AlleleFrequencyPosteriors,
int AFofMaxLikelihood); int AFofMaxLikelihood);
protected int getUnfilteredDepth(ReadBackedPileup pileup) { protected int getFilteredDepth(ReadBackedPileup pileup) {
int count = 0; int count = 0;
for ( PileupElement p : pileup ) { for ( PileupElement p : pileup ) {
if ( DiploidSNPGenotypeLikelihoods.usableBase(p, true) ) if ( DiploidSNPGenotypeLikelihoods.usableBase(p, true) )

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -224,7 +224,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
HashMap<String, Object> attributes = new HashMap<String, Object>(); HashMap<String, Object> attributes = new HashMap<String, Object>();
ArrayList<Allele> myAlleles = new ArrayList<Allele>(); ArrayList<Allele> myAlleles = new ArrayList<Allele>();
attributes.put(VCFConstants.DEPTH_KEY, getUnfilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup())); attributes.put(VCFConstants.DEPTH_KEY, getFilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup()));
double qual; double qual;
double[] posteriors = GLs.get(sample).getPosteriors(); double[] posteriors = GLs.get(sample).getPosteriors();

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
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@ -125,7 +125,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
} }
HashMap<String, Object> attributes = new HashMap<String, Object>(); HashMap<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VCFConstants.DEPTH_KEY, getUnfilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup())); attributes.put(VCFConstants.DEPTH_KEY, getFilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup()));
GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods()); GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods());
attributes.put(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, likelihoods.getAsString()); attributes.put(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, likelihoods.getAsString());