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For Kiran: warn the user when the actual and vcf ref bases differ so that if an exception is generated later, he knows why. All: should we generate the actual exception here? Is there any reason to allow cases where the vcf record has a different ref base than the actual reference? I'd vote that we die here. Thoughts? 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3680 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-06-30 13:56:16 +00:00
parent d932322190
commit 8fb37f5f7a
1 changed files with 2 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -214,6 +214,8 @@ public class VariantContextAdaptors {
// refAllele = Allele.create(vcf.getReference(), true);
} else if ( !vcf.isIndel() ) {
refAllele = Allele.create(ref.getBase(), true);
if ( (char)ref.getBase() != vcf.getReference().charAt(0) )
System.err.println("\n*** WARN: The VCF reference base (" + vcf.getReference().charAt(0) + ") doesn't match the actual reference base (" + (char)ref.getBase() + "); there is a good chance this will generate an exception!");
} else if ( vcf.isDeletion() ) {
int start = vcf.getPosition() - (int)ref.getWindow().getStart() + 1;
int delLength = 0;