Program: 100660
Project: 100660
Buggy source:
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes atts) throws SAXException {
  handleRootElement(atts);
  String processingRole=atts.getValue(ATTRIBUTE_NAME_PROCESSING_ROLE);
  if (processingRole == null) {
    processingRole=processRoleStack.peek();
  }
  processRoleStack.push(processingRole);
  final URI href=toURI(atts.getValue(ATTRIBUTE_NAME_HREF));
  final String scope=atts.getValue(ATTRIBUTE_NAME_SCOPE);
  if (href != null && !ATTR_SCOPE_VALUE_EXTERNAL.equals(scope)) {
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equals(processingRole)) {
      resourceOnlySet.add(currentDir.resolve(href));
    }
 else {
      normalProcessingRoleSet.add(currentDir.resolve(href));
    }
  }
  final String classValue=atts.getValue(ATTRIBUTE_NAME_CLASS);
  if (SUBJECTSCHEME_SUBJECTSCHEME.matches(classValue)) {
    final URI key=ROOT_URI;
    final Set<URI> children=schemeRelationGraph.containsKey(key) ? schemeRelationGraph.get(key) : new LinkedHashSet<URI>();
    children.add(currentFile);
    schemeRelationGraph.put(key,children);
    schemeRefSet.add(currentFile);
  }
 else   if (SUBJECTSCHEME_SCHEMEREF.matches(classValue)) {
    if (href != null) {
      final URI key=currentFile;
      final Set<URI> children=schemeRelationGraph.containsKey(key) ? schemeRelationGraph.get(key) : new LinkedHashSet<URI>();
      final URI child=currentFile.resolve(href);
      children.add(child);
      schemeRelationGraph.put(key,children);
    }
  }
  if (foreignLevel > 0) {
    foreignLevel++;
    return;
  }
 else   if (TOPIC_FOREIGN.matches(classValue) || TOPIC_UNKNOWN.matches(classValue)) {
    foreignLevel++;
  }
  if (chunkLevel > 0) {
    chunkLevel++;
  }
 else   if (atts.getValue(ATTRIBUTE_NAME_CHUNK) != null) {
    chunkLevel++;
  }
  if (relTableLevel > 0) {
    relTableLevel++;
  }
 else   if (MAP_RELTABLE.matches(classValue)) {
    relTableLevel++;
  }
  if (chunkToNavLevel > 0) {
    chunkToNavLevel++;
  }
 else   if (atts.getValue(ATTRIBUTE_NAME_CHUNK) != null && atts.getValue(ATTRIBUTE_NAME_CHUNK).contains(CHUNK_TO_NAVIGATION)) {
    chunkToNavLevel++;
  }
  if (topicGroupLevel > 0) {
    topicGroupLevel++;
  }
 else   if (MAPGROUP_D_TOPICGROUP.matches(classValue)) {
    topicGroupLevel++;
  }
  if (classValue == null && !ELEMENT_NAME_DITA.equals(localName)) {
    logger.info(MessageUtils.getInstance().getMessage("String_Node_Str",localName).toString());
  }
  if (TOPIC_TOPIC.matches(classValue)) {
    final String domains=atts.getValue(ATTRIBUTE_NAME_DOMAINS);
    if (domains == null) {
      logger.info(MessageUtils.getInstance().getMessage("String_Node_Str",localName).toString());
    }
  }
  if ((MAP_MAP.matches(classValue)) || (TOPIC_TITLE.matches(classValue))) {
    isValidInput=true;
  }
  parseConrefAttr(atts);
  parseAttribute(atts,ATTRIBUTE_NAME_HREF);
  parseAttribute(atts,ATTRIBUTE_NAME_COPY_TO);
  parseAttribute(atts,ATTRIBUTE_NAME_DATA);
  parseConactionAttr(atts);
  parseConkeyrefAttr(atts);
  parseKeyrefAttr(atts);
  getContentHandler().startElement(uri,localName,qName,atts);
}

Fixed version (ground truth):
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes atts) throws SAXException {
  handleRootElement(atts);
  String processingRole=atts.getValue(ATTRIBUTE_NAME_PROCESSING_ROLE);
  if (processingRole == null) {
    processingRole=processRoleStack.peek();
  }
  processRoleStack.push(processingRole);
  final URI href=toURI(atts.getValue(ATTRIBUTE_NAME_HREF));
  final String scope=atts.getValue(ATTRIBUTE_NAME_SCOPE);
  if (href != null && !ATTR_SCOPE_VALUE_EXTERNAL.equals(scope)) {
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equals(processingRole)) {
      resourceOnlySet.add(stripFragment(currentDir.resolve(href)));
    }
 else {
      normalProcessingRoleSet.add(stripFragment(currentDir.resolve(href)));
    }
  }
  final String classValue=atts.getValue(ATTRIBUTE_NAME_CLASS);
  if (SUBJECTSCHEME_SUBJECTSCHEME.matches(classValue)) {
    final URI key=ROOT_URI;
    final Set<URI> children=schemeRelationGraph.containsKey(key) ? schemeRelationGraph.get(key) : new LinkedHashSet<URI>();
    children.add(currentFile);
    schemeRelationGraph.put(key,children);
    schemeRefSet.add(currentFile);
  }
 else   if (SUBJECTSCHEME_SCHEMEREF.matches(classValue)) {
    if (href != null) {
      final URI key=currentFile;
      final Set<URI> children=schemeRelationGraph.containsKey(key) ? schemeRelationGraph.get(key) : new LinkedHashSet<URI>();
      final URI child=currentFile.resolve(href);
      children.add(child);
      schemeRelationGraph.put(key,children);
    }
  }
  if (foreignLevel > 0) {
    foreignLevel++;
    return;
  }
 else   if (TOPIC_FOREIGN.matches(classValue) || TOPIC_UNKNOWN.matches(classValue)) {
    foreignLevel++;
  }
  if (chunkLevel > 0) {
    chunkLevel++;
  }
 else   if (atts.getValue(ATTRIBUTE_NAME_CHUNK) != null) {
    chunkLevel++;
  }
  if (relTableLevel > 0) {
    relTableLevel++;
  }
 else   if (MAP_RELTABLE.matches(classValue)) {
    relTableLevel++;
  }
  if (chunkToNavLevel > 0) {
    chunkToNavLevel++;
  }
 else   if (atts.getValue(ATTRIBUTE_NAME_CHUNK) != null && atts.getValue(ATTRIBUTE_NAME_CHUNK).contains(CHUNK_TO_NAVIGATION)) {
    chunkToNavLevel++;
  }
  if (topicGroupLevel > 0) {
    topicGroupLevel++;
  }
 else   if (MAPGROUP_D_TOPICGROUP.matches(classValue)) {
    topicGroupLevel++;
  }
  if (classValue == null && !ELEMENT_NAME_DITA.equals(localName)) {
    logger.info(MessageUtils.getInstance().getMessage("String_Node_Str",localName).toString());
  }
  if (TOPIC_TOPIC.matches(classValue)) {
    final String domains=atts.getValue(ATTRIBUTE_NAME_DOMAINS);
    if (domains == null) {
      logger.info(MessageUtils.getInstance().getMessage("String_Node_Str",localName).toString());
    }
  }
  if ((MAP_MAP.matches(classValue)) || (TOPIC_TITLE.matches(classValue))) {
    isValidInput=true;
  }
  parseConrefAttr(atts);
  parseAttribute(atts,ATTRIBUTE_NAME_HREF);
  parseAttribute(atts,ATTRIBUTE_NAME_COPY_TO);
  parseAttribute(atts,ATTRIBUTE_NAME_DATA);
  parseConactionAttr(atts);
  parseConkeyrefAttr(atts);
  parseKeyrefAttr(atts);
  getContentHandler().startElement(uri,localName,qName,atts);
}