From 7a3a464959c8ef75a0eb7fda7e1136aaef6b18bc Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Nov 2010 14:02:09 +0000
Subject: [PATCH] Finally, the logic is right

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4674 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 e75766e12..40678ec58 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.isNotFiltered() ) ) {
+                if ( (! ignoreMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
                     List<String> vals = extractFields(vc, fieldsToTake);
 
                     out.println(Utils.join("\t", vals));