From 54a9bc2da2c005afb110eb53c49392a434c7f0dd Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 28 Apr 2012 09:12:26 -0400
Subject: [PATCH] Bug fix in reverse trim alleles for the case of mixed records
 that become non-mixed after subsetting the alleles.

---
 .../sting/utils/variantcontext/VariantContextUtils.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 85ba71f1a..92915faaf 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -839,7 +839,7 @@ public class VariantContextUtils {
             genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles));
         }
 
-        return new VariantContextBuilder(inputVC).stop(inputVC.getEnd() - trimExtent).alleles(alleles).genotypes(genotypes).make();
+        return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() + (inputVC.isMixed() ? -1 : 0)).alleles(alleles).genotypes(genotypes).make();
     }
 
     public static GenotypesContext stripPLs(GenotypesContext genotypes) {