From 85714621be48703a434a5744bc654847f4e7f2f2 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 4 Jan 2011 21:48:14 +0000 Subject: [PATCH] Better interface to Genotypelikelihoods class. Now you need to specify the format (GL vs PL) of the output string when calling getAsString(). All likelihoods are represented as GLs internally. QualByDepth no longer does its own conversion. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4933 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/annotator/QualByDepth.java | 8 +------- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 4 ++-- 2 files changed, 3 insertions(+), 9 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index f37f42cd0..56219ed1e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -47,13 +47,7 @@ public class QualByDepth implements InfoFieldAnnotation, StandardAnnotation { if ( genotype.getValue().hasLikelihoods() ) { GenotypeLikelihoods GLs = genotype.getValue().getLikelihoods(); - double[] likelihoods = GLs.getAsVector(); - if ( GLs.getKey() == VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY ) { - for (int i = 0; i < likelihoods.length; i++) - likelihoods[i] /= -10.0; - } - - qual += 10.0 * getQual(likelihoods); + qual += 10.0 * getQual(GLs.getAsVector()); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 6869cd1cb..b8a4b09de 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -213,9 +213,9 @@ public class UnifiedGenotyperEngine { } HashMap attributes = new HashMap(); - GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods(), VCFConstants.GENOTYPE_LIKELIHOODS_KEY); + GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods()); attributes.put(VCFConstants.DEPTH_KEY, GL.getDepth()); - attributes.put(likelihoods.getKey(), likelihoods); + attributes.put(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, likelihoods); genotypes.put(GL.getSample(), new Genotype(GL.getSample(), noCall, Genotype.NO_NEG_LOG_10PERROR, null, attributes, false)); }