From 5bdcc2b4dc7de8dc2029c659e1adfa3356b7baf5 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 7 Oct 2009 18:46:51 +0000
Subject: [PATCH] Included HLA class 2 genes in CreatePedFileWalker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1776 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
index 7669d42f1..3d03e7c36 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
@@ -209,8 +209,9 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
                 error = error + PrintGenotypes(s[1], HLA_DQB1_1,HLA_DQB1_2, HLA_DQB1_start,HLA_DQB1_end);
                 error = error + PrintGenotypes(s[1], HLA_DPA1_1,HLA_DPA1_2, HLA_DPA1_start,HLA_DPA1_end);
                 error = error + PrintGenotypes(s[1], HLA_DPB1_1,HLA_DPB1_2, HLA_DPB1_start,HLA_DPB1_end);
-                out.printf("%s",error);
+                
                 out.printf("\n");
+                out.printf("%s",error);
             }
         }