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-VCF writer now checks whether the allele frequency has been set before trying to write it out. 

-Renamed methods to be more consistent.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-02 16:25:32 +00:00
parent 6231637615
commit 2838629724
5 changed files with 17 additions and 6 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java
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@ -78,7 +78,7 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
((SLODBacked)locusdata).setSLOD(strandScore);
}
locusdata.setAlleleFrequency(overall.getMAF());
locusdata.setNonRefAlleleFrequency(overall.getMAF());
}
return new Pair<List<Genotype>, GenotypeLocusData>(genotypeCallsFromGenotypeLikelihoods(overall, ref, contexts), locusdata);
}

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
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@ -323,7 +323,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
GenotypeLocusData locusdata = GenotypeWriterFactory.createSupportedGenotypeLocusData(OUTPUT_FORMAT, ref, loc, VARIANT_TYPE.SNP);
if ( locusdata != null ) {
locusdata.addAlternateAllele(bestAlternateAllele.toString());
locusdata.setAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1));
locusdata.setNonRefAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1));
if ( locusdata instanceof ConfidenceBacked ) {
((ConfidenceBacked)locusdata).setConfidence(phredScaledConfidence);
}

8
java/src/org/broadinstitute/sting/utils/genotype/GenotypeLocusData.java
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@ -16,10 +16,16 @@ public interface GenotypeLocusData extends Variation {
*/
public void addAlternateAllele(String alt);
/**
*
* @return true if the allele frequency has been set
*/
public boolean hasNonRefAlleleFrequency();
/**
*
* @param frequency the allele frequency for this genotype
*/
public void setAlleleFrequency(double frequency);
public void setNonRefAlleleFrequency(double frequency);
}

8
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeLocusData.java
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@ -21,7 +21,7 @@ public class VCFGenotypeLocusData implements GenotypeLocusData, ConfidenceBacked
private Double mSLOD = null;
// the allele frequency field
private double mAlleleFrequency = 0.0;
private double mAlleleFrequency = -1.0;
// the location
private GenomeLoc mLoc;
@ -97,6 +97,10 @@ public class VCFGenotypeLocusData implements GenotypeLocusData, ConfidenceBacked
return mType;
}
public boolean hasNonRefAlleleFrequency() {
return mAlleleFrequency >= 0.0;
}
public double getNonRefAlleleFrequency() {
return mAlleleFrequency;
}
@ -171,7 +175,7 @@ public class VCFGenotypeLocusData implements GenotypeLocusData, ConfidenceBacked
*
* @param frequency the allele frequency for this genotype
*/
public void setAlleleFrequency(double frequency) {
public void setNonRefAlleleFrequency(double frequency) {
mAlleleFrequency = frequency;
}

3
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
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@ -190,7 +190,8 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
if ( locusdata != null ) {
if ( locusdata.getSLOD() != null )
infoFields.put("SB", String.format("%.2f", locusdata.getSLOD()));
infoFields.put("AF", String.format("%.2f", locusdata.getNonRefAlleleFrequency()));
if ( locusdata.hasNonRefAlleleFrequency() )
infoFields.put("AF", String.format("%.2f", locusdata.getNonRefAlleleFrequency()));
Map<String, String> otherFields = locusdata.getFields();
if ( otherFields != null ) {
infoFields.putAll(otherFields);