From da4af3b620b41ce63a4fa549c11ecffc21c21dc4 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Jul 2009 15:59:18 +0000
Subject: [PATCH] print indels in the format required for 1KG submissions

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1275 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
index 6cb8c7cda..020c9f39b 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
@@ -37,7 +37,9 @@ public class SimpleIndelROD extends TabularROD implements Genotype {
 
     public String toString() {
         StringBuffer sb = new StringBuffer();
-        sb.append(getLocation() + "\t" + getFWDAlleles().get(0));
+        sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");
+        String indel = getFWDAlleles().get(0);
+        sb.append((indel.length()-1) + "\t" + (isInsertion() ? "I" : "D") + "\t" + indel.substring(1));
         return sb.toString();
     }
  }
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