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Bug fix for PL vs. GL in header. PL now truly default output for UGv2 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4592 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-10-28 12:39:18 +00:00
parent 9782dde3dd
commit 860de05a7c
2 changed files with 4 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
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@ -127,7 +127,7 @@ 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, getFilteredDepth(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(), UnifiedGenotyperV2.DEFAULT_GENOTYPE_LIKELIHOODS_KEY);
attributes.put(likelihoods.getKey(), likelihoods.getAsString()); attributes.put(likelihoods.getKey(), likelihoods.getAsString());
calls.put(sample, new Genotype(sample, myAlleles, AFbasedGenotype.second, null, attributes, false)); calls.put(sample, new Genotype(sample, myAlleles, AFbasedGenotype.second, null, attributes, false));

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
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@ -49,6 +49,8 @@ import java.io.PrintStream;
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250) @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
public class UnifiedGenotyperV2 extends LocusWalker<VariantCallContext, UnifiedGenotyperV2.UGStatistics> implements TreeReducible<UnifiedGenotyperV2.UGStatistics> { public class UnifiedGenotyperV2 extends LocusWalker<VariantCallContext, UnifiedGenotyperV2.UGStatistics> implements TreeReducible<UnifiedGenotyperV2.UGStatistics> {
public static final String DEFAULT_GENOTYPE_LIKELIHOODS_KEY = VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY;
@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
@ -156,7 +158,7 @@ public class UnifiedGenotyperV2 extends LocusWalker<VariantCallContext, UnifiedG
} }
// FORMAT and INFO fields // FORMAT and INFO fields
headerInfo.addAll(VCFUtils.getSupportedHeaderStrings(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)); headerInfo.addAll(VCFUtils.getSupportedHeaderStrings(UnifiedGenotyperV2.DEFAULT_GENOTYPE_LIKELIHOODS_KEY));
// FILTER fields // FILTER fields
if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING || if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING ||