From dbde721dd0166d1f466ad83becf0e9b9f6ba551f Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 11 Nov 2010 18:54:51 +0000
Subject: [PATCH] Bug fix for filtered records

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4651 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/VariantsToTable.java        | 2 +-
 1 file changed, 1 insertion(+), 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 7787c37d0..f39ca00d2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -117,7 +117,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
             Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
             for ( VariantContext vc : vcs) {
-                if ( ! ignoreMultiAllelic || vc.isBiallelic() || ( !showFiltered || !vc.isFiltered() ) ) {
+                if ( ! ignoreMultiAllelic || vc.isBiallelic() || ( showFiltered || ! vc.isNotFiltered() ) ) {
                     List<String> vals = extractFields(vc, fieldsToTake);
 
                     out.println(Utils.join("\t", vals));