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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@4591 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-10-28 12:38:48 +00:00
parent fe3cfb067c
commit 9782dde3dd
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
View File

@ -257,7 +257,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
attributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,String.format("%4.2f", 10*qual)); attributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,String.format("%4.2f", 10*qual));
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, qual, null, attributes, false)); calls.put(sample, new Genotype(sample, myAlleles, qual, null, attributes, false));

2
java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java
View File

@ -176,7 +176,7 @@ public class VCFUtils {
if ( glType == VCFConstants.GENOTYPE_LIKELIHOODS_KEY ) if ( glType == VCFConstants.GENOTYPE_LIKELIHOODS_KEY )
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic")); result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"));
else if ( glType == VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY ) else if ( glType == VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY )
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic")); result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"));
else else
throw new ReviewedStingException("Unexpected GL type " + glType); throw new ReviewedStingException("Unexpected GL type " + glType);