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Bugfix for new PASS position in dictionary in BCF2

This commit is contained in:
Mark DePristo 2012-08-03 09:42:21 -04:00
parent d22b8cf86b
commit e04989f76d
1 changed files with 3 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
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@ -77,7 +77,9 @@ public final class BCF2Utils {
final Set<String> seen = new HashSet<String>(); final Set<String> seen = new HashSet<String>();
final ArrayList<String> dict = new ArrayList<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 // set up the strings dictionary
for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) { for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {