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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
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ebanks 2010-01-03 22:02:39 +00:00
parent b668d32cf1
commit 7b702b086f
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
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@ -248,8 +248,8 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
} }
public double getNonRefAlleleFrequency() { public double getNonRefAlleleFrequency() {
if ( !isBiallelic() ) if ( isReference() )
throw new StingException("This VCF record is not bi-allelic."); throw new StingException("This VCF record is not variant.");
if ( mInfoFields.containsKey(ALLELE_FREQUENCY_KEY) ) { if ( mInfoFields.containsKey(ALLELE_FREQUENCY_KEY) ) {
return Double.valueOf(mInfoFields.get(ALLELE_FREQUENCY_KEY)); return Double.valueOf(mInfoFields.get(ALLELE_FREQUENCY_KEY));