From 6d07181dc99a3e41380c80b7197ddc1648fd7bfc Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Sep 2010 19:18:45 +0000
Subject: [PATCH] When processing Beagle output and creating new vcf, output
 the filtered records in the original input vcf as is, so that we don't lose
 the information on them when we run Beagle.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4276 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index 9261304fa..9d530e218 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -124,6 +124,10 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
         if ( vc_input == null  )
             return 0;
 
+        if (vc_input.isFiltered()) {
+            vcfWriter.add(vc_input, ref.getBase());
+            return 1;
+        }
         List<Object> r2rods = tracker.getReferenceMetaData(R2_ROD_NAME);
 
         // ignore places where we don't have a variant