From 753cb100a3a39bb7ba5db528f4a127b09f3c4a7c Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 23 Nov 2009 02:14:25 +0000 Subject: [PATCH] Add checks for weird situations git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2115 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/annotator/AlleleBalance.java | 4 ++++ .../sting/gatk/walkers/annotator/OnOffGenotype.java | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index 15278bef8..b87243547 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -93,6 +93,10 @@ public class AlleleBalance implements VariantAnnotation { int refCount = counts[BaseUtils.simpleBaseToBaseIndex(ref)]; int altCount = counts[BaseUtils.simpleBaseToBaseIndex(altBase)]; + // sanity check + if ( refCount + altCount == 0 ) + continue; + double[] posteriors = ((PosteriorsBacked)g).getPosteriors(); posteriors = MathUtils.normalizeFromLog10(posteriors); weights.add(posteriors[bestGenotype.ordinal()]); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java index 17b945dba..32d319dd6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java @@ -97,6 +97,10 @@ public class OnOffGenotype implements VariantAnnotation { for (int i = 0; i < counts.length; i++) totalCount += counts[i]; + // sanity check + if ( totalCount == 0 ) + continue; + double[] posteriors = ((PosteriorsBacked)g).getPosteriors(); posteriors = MathUtils.normalizeFromLog10(posteriors); weights.add(posteriors[bestGenotype.ordinal()]);