From 7b702b086fecb1e81aa8093c6e6a7127f649397d Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 3 Jan 2010 22:02:39 +0000 Subject: [PATCH] You don't need to be bi-allelic to have a non-ref alt allele frequnecy, but you do have to be a variant. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2495 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/utils/genotype/vcf/VCFRecord.java | 4 ++-- 1 file changed, 2 insertions(+), 2 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 fc9752629..6650f99ea 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java @@ -248,8 +248,8 @@ public class VCFRecord implements Variation, VariantBackedByGenotype { } public double getNonRefAlleleFrequency() { - if ( !isBiallelic() ) - throw new StingException("This VCF record is not bi-allelic."); + 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));