From 8e83b6646ba9934c8c9475538e984d684b2d37eb Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 17 Aug 2011 21:49:14 -0400 Subject: [PATCH] Bug fix for Chris: don't validate ref base for complex events. --- .../sting/utils/variantcontext/VariantContext.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 ca3399c78..dacc2d94a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1080,8 +1080,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati } public void validateReferenceBases(Allele reference, Byte paddedRefBase) { - // don't validate if we're an insertion - if ( !reference.isNull() && !reference.basesMatch(getReference()) ) { + // don't validate if we're an insertion or complex event + if ( !reference.isNull() && getReference().length() == 1 && !reference.basesMatch(getReference()) ) { throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString())); }