diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index eac6d70b5..14a680af4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1357,10 +1357,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati throw new IllegalArgumentException("Duplicate allele added to VariantContext: " + a); } - // deal with the case where the first allele isn't the reference + // deal with the case where the first allele isn't the reference if ( a.isReference() ) { if ( sawRef ) - throw new IllegalArgumentException("Alleles for a VariantContext must contain a single reference allele: " + alleles); + throw new IllegalArgumentException("Alleles for a VariantContext must contain at most one reference allele: " + alleles); alleleList.add(0, a); sawRef = true; } @@ -1372,7 +1372,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati throw new IllegalArgumentException("Cannot create a VariantContext with an empty allele list"); if ( alleleList.get(0).isNonReference() ) - throw new IllegalArgumentException("Alleles for a VariantContext must contain a single reference allele: " + alleles); + throw new IllegalArgumentException("Alleles for a VariantContext must contain at least one reference allele: " + alleles); return alleleList; }