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 seen = new HashSet(); final ArrayList dict = new ArrayList(); - 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() ) {