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Better error when bad ref bases are provided 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4414 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-03 05:40:37 +00:00
parent 40b2f62a83
commit 490e5e1b0f
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -449,7 +449,7 @@ public class VariantContextUtils {
if ( ref == null || ref.length() < myRef.length() ) if ( ref == null || ref.length() < myRef.length() )
ref = myRef; ref = myRef;
else if ( ref.length() == myRef.length() && ! ref.equals(myRef) ) else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
throw new ReviewedStingException("BUG: equal length references with difference bases: "+ ref + " " + myRef); throw new UserException.BadInput(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef));
} }
return ref; return ref;