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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
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depristo 2010-01-07 01:18:30 +00:00
parent 7215526810
commit a9245a58e2
1 changed files with 0 additions and 3 deletions
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3
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
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@ -253,9 +253,6 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
} }
public double getNonRefAlleleFrequency() { public double getNonRefAlleleFrequency() {
if ( isReference() )
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));
} else { } else {