Program: 154157
Project: 154157
Buggy source:
@Override public void merge(String prefix){
  logger.info("String_Node_Str" + sourceFile);
  sourceUtils=new OBOUtils(sourceFile.getAbsolutePath());
  logger.info("String_Node_Str");
  int termCount=0;
  int synCount=0;
  target.updateIDGenerator(prefix);
  Collection<OBOClass> allTerms=sourceUtils.getTerms();
  for (  OBOClass term : allTerms) {
    Term matchingTerm=target.getTermbyName(term.getName());
    if (matchingTerm != null) {
      termCount++;
      for (      Synonym syn : term.getSynonyms()) {
        if (syn.getSynonymType().equals(sourceUtils.getCommonNameType())) {
          if (!syn.getXrefs().isEmpty()) {
            final Dbxref ref=syn.getXrefs().iterator().next();
            SynonymI newSyn=target.makeCommonNameWithXref(syn.getText(),ref.getDatabase(),ref.getDatabaseID());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
 else {
            SynonymI newSyn=target.makeCommonName(syn.getText());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
        }
 else {
          if (!syn.getXrefs().isEmpty()) {
            final Dbxref ref=syn.getXrefs().iterator().next();
            SynonymI newSyn=target.makeSynonymWithXref(syn.getText(),ref.getDatabase(),ref.getDatabaseID());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
 else {
            SynonymI newSyn=target.makeSynonym(syn.getText());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
        }
      }
    }
    if (termCount % 1000 == 0) {
      logger.info("String_Node_Str" + termCount + "String_Node_Str"+ synCount+ "String_Node_Str");
    }
  }
}

Fixed version (ground truth):
@Override public void merge(String prefix){
  logger.info("String_Node_Str" + sourceFile);
  sourceUtils=new OBOUtils(sourceFile.getAbsolutePath());
  logger.info("String_Node_Str");
  int termCount=0;
  int synCount=0;
  target.updateIDGenerator(prefix);
  Collection<OBOClass> allTerms=sourceUtils.getTerms();
  for (  OBOClass term : allTerms) {
    Term matchingTerm=target.getTermbyName(term.getName());
    if (matchingTerm != null) {
      termCount++;
      for (      Synonym syn : term.getSynonyms()) {
        if (sourceUtils.getCommonNameType().equals(syn.getSynonymType())) {
          if (!syn.getXrefs().isEmpty()) {
            final Dbxref ref=syn.getXrefs().iterator().next();
            SynonymI newSyn=target.makeCommonNameWithXref(syn.getText(),ref.getDatabase(),ref.getDatabaseID());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
 else {
            SynonymI newSyn=target.makeCommonName(syn.getText());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
        }
 else {
          if (!syn.getXrefs().isEmpty()) {
            final Dbxref ref=syn.getXrefs().iterator().next();
            SynonymI newSyn=target.makeSynonymWithXref(syn.getText(),ref.getDatabase(),ref.getDatabaseID());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
 else {
            SynonymI newSyn=target.makeSynonym(syn.getText());
            matchingTerm.addSynonym(newSyn);
            synCount++;
          }
        }
      }
    }
    if (termCount % 1000 == 0) {
      logger.info("String_Node_Str" + termCount + "String_Node_Str"+ synCount+ "String_Node_Str");
    }
  }
}