From e04989f76d3b2771f83cb33900c31a5518503e36 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 3 Aug 2012 09:42:21 -0400
Subject: [PATCH] Bugfix for new PASS position in dictionary in BCF2

---
 .../org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
index d3f3fc102..c79abe2ae 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
@@ -77,7 +77,9 @@ public final class BCF2Utils {
         final Set<String> seen = new HashSet<String>();
         final ArrayList<String> dict = new ArrayList<String>();
 
-        dict.add(VCFConstants.PASSES_FILTERS_v4); // special case the special PASS field
+        // special case the special PASS field which doesn't show up in the FILTER field definitions
+        seen.add(VCFConstants.PASSES_FILTERS_v4);
+        dict.add(VCFConstants.PASSES_FILTERS_v4);
 
         // set up the strings dictionary
         for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {