From 1675bd4dd7041c4659a5c217780d76fa5b26f182 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 13 Mar 2012 10:55:52 -0400
Subject: [PATCH] When creating a synthetic VC based on the passed in alleles,
 set the length correctly.

---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 05a977add..c077cf774 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -253,7 +253,7 @@ public class UnifiedGenotyperEngine {
             VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
             if ( vcInput == null )
                 return null;
-            vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), vcInput.getAlleles()).make();
+            vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()).make();
         } else {
             // deal with bad/non-standard reference bases
             if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )