From 70ba851478a1805509d306a8514c192b57b38e6b Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 29 Jun 2011 15:59:10 -0400
Subject: [PATCH] Might as well check for the illegal state and throw an
 exception

---
 .../sting/gatk/walkers/indels/IndelRealigner.java               | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 33de08bb6..3cfa58c02 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -1010,6 +1010,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             for ( byte b : indelStr )
                 sb.append((char)b);
             cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
+        } else {
+            throw new ReviewedStingException("Creating an alternate consensus from a complex indel is not allowed");
         }
 
         if ( reference.length - refIdx > 0 )