From 79bc8180228480f037a122b609b24ff666a7040f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 16 Jan 2013 16:15:58 -0500
Subject: [PATCH] Bug fix for VariantsToVCF: old dbSNP files can have '-' as
 reference base and those records always need to be padded.

---
 .../sting/gatk/refdata/VariantContextAdaptors.java           | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index c7edebd81..a77341a5d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -194,17 +194,18 @@ public class VariantContextAdaptors {
                 return null; // we weren't given enough reference context to create the VariantContext
 
             final byte refBaseForIndel = ref.getBases()[index];
+            final boolean refBaseIsDash = dbsnp.getNCBIRefBase().equals("-");
 
             boolean addPaddingBase;
             if ( isSNP(dbsnp) || isMNP(dbsnp) )
                 addPaddingBase = false;
             else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") )
-                addPaddingBase = VariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp)));
+                addPaddingBase = refBaseIsDash || VariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp)));
             else
                 return null; // can't handle anything else
 
             Allele refAllele;
-            if ( dbsnp.getNCBIRefBase().equals("-") )
+            if ( refBaseIsDash )
                 refAllele = Allele.create(refBaseForIndel, true);
             else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
                 return null;