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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
This commit is contained in:
melonistic 2015-04-26 16:58:09 -04:00
parent 28a7ea43ec
commit 8d25b2ba40
1 changed files with 2 additions and 6 deletions
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8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
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@ -250,12 +250,8 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
final GenomeLoc loc = genomeLocParser.createGenomeLoc(vc);
final List<Allele> 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);