From 8d25b2ba4056b8f43c8babae924a1783b09bced4 Mon Sep 17 00:00:00 2001 From: melonistic Date: Sun, 26 Apr 2015 16:58:09 -0400 Subject: [PATCH] removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841 removed irrelevant -0 comments as specified in issue #841 but committed in #973 --- .../gatk/tools/walkers/genotyper/GenotypingEngine.java | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java index 8dd616f41..2439e6219 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java @@ -250,12 +250,8 @@ public abstract class GenotypingEngine outputAlleles = outputAlternativeAlleles.outputAlleles(vc.getReference()); final VariantContextBuilder builder = new VariantContextBuilder(callSourceString(), loc.getContig(), loc.getStart(), loc.getStop(), outputAlleles); - - // Seems that when log10PError is 0.0, you must pass -0.0 to get a nice output at the other end otherwise is a "-0". - // Truth is that this should be fixed in the "variant" dependency code but perhaps it can be amended also in the VariantContextWriter. - //TODO Please remove this comment when this has been fixed (PT https://www.pivotaltracker.com/story/show/69492530) - //TODO and change the code below accordingly. - builder.log10PError(log10Confidence == 0.0 ? -0.0 : log10Confidence); + + builder.log10PError(log10Confidence); if ( ! passesCallThreshold(phredScaledConfidence) ) builder.filter(GATKVCFConstants.LOW_QUAL_FILTER_NAME);