From 8719dde59dfe8f39ec8f3e2d7e8b29e0dd49115a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 21 Sep 2010 13:16:41 +0000
Subject: [PATCH] Now prints out PASS when a variant is unfiltered

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4318 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/VariantsToTable.java      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 4e23d4d62..e1c415183 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -87,7 +87,9 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
             }
         });
         getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
-        getters.put("FILTER", new Getter() { public String get(VariantContext vc) { return Utils.join(",", vc.getFilters()); } });
+        getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
+            return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); } 
+        });
 
         getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
         getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });