From 3adf7fbf64c98a27bcc472a9b1c54998070d91d2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 23 Apr 2010 13:52:51 +0000
Subject: [PATCH] bug fix for known-indels used as consenses

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java   | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

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 4b7531401..6be4590d4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -716,11 +716,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 break;
             case I:
                 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;
-                   }
+                    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;
@@ -759,7 +759,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             cigar.add(new CigarElement(indelStr.length, CigarOperator.D));
         }
         else {
-            sb.append(indelStr);
+            for ( byte b : indelStr )
+                sb.append((char)b);
             cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
         }