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I just wanted one more vote. It's settled: we die. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3681 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-06-30 14:00:56 +00:00
parent 8fb37f5f7a
commit ae33d8a2f2
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -215,7 +215,7 @@ public class VariantContextAdaptors {
} 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!");
throw new StingException("The VCF reference base (" + vcf.getReference().charAt(0) + ") doesn't match the actual reference base (" + (char)ref.getBase() + "); please check that you are using the appropriate reference file");
} else if ( vcf.isDeletion() ) {
int start = vcf.getPosition() - (int)ref.getWindow().getStart() + 1;
int delLength = 0;