From d73bc490c25a7c4f217bd6ca437315cbca802694 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 24 Feb 2010 03:00:26 +0000
Subject: [PATCH] Do not build alt consensuses from insertions that have an N
 in the inserted sequence. Seems to cause problems rather than solve any

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2880 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java         | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 51e39d768..aa746a757 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -676,8 +676,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 altIdx += elementLength;
                 break;
             case I:
-                for (int j = 0; j < elementLength; j++)
+                for (int j = 0; j < elementLength; j++) {
+                   if ( ! BaseUtils.isRegularBase(readStr[altIdx+j]) ) {
+                       // Insertions with N's in them cause real problems sometimes; it's better to drop them altogether
+                       ok_flag=false;
+                       break;
+                   }
                     sb.append((char)readStr[altIdx + j]);
+                }
                 altIdx += elementLength;
                 indelCount++;
                 break;