From a9245a58e2645eabe85f846e8710077758509e77 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 7 Jan 2010 01:18:30 +0000 Subject: [PATCH] Fix for incorrect exception throwing in VCFRecord. It is reasonable to ask for the non-ref allele freq at all ref sites. Was only passing in tests because isReference was broken git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2532 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java index 527c39946..20d60e52f 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java @@ -253,9 +253,6 @@ public class VCFRecord implements Variation, VariantBackedByGenotype { } public double getNonRefAlleleFrequency() { - if ( isReference() ) - throw new StingException("This VCF record is not variant."); - if ( mInfoFields.containsKey(ALLELE_FREQUENCY_KEY) ) { return Double.valueOf(mInfoFields.get(ALLELE_FREQUENCY_KEY)); } else {