From f6648e01446e699735e1d502c2d03a1b44f3771c Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 3 Aug 2011 12:03:50 -0400
Subject: [PATCH] Don't left-align complex indels because it's too complicated.

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 5ff3921de..5ab326418 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -90,7 +90,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
 
 
     private int alignAndWrite(VariantContext vc, final ReferenceContext ref) {
-        if ( vc.isBiallelic() && vc.isIndel() )
+        if ( vc.isBiallelic() && vc.isIndel() && !vc.isComplexIndel() )
             return writeLeftAlignedIndel(vc, ref);
         else {
             writer.add(vc);