From a68e6810c90711d88d2a829d27818034f721eb12 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 14 Nov 2012 14:45:15 -0500 Subject: [PATCH] Back off experimental code that escaped last commit, not for general use yet --- .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 22ed95365..80bc04845 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -190,8 +190,9 @@ public class UnifiedGenotyperEngine { final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap); if ( vc != null ) results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap)); - else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES) - results.add(generateEmptyContext(tracker, refContext, null, rawContext)); +// todo - uncomment if we want to also emit a null ref call (with no QUAL) if there's no evidence for REF and if EMIT_ALL_SITES is set +// else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES) +// results.add(generateEmptyContext(tracker, refContext, null, rawContext)); } }