Program: 100727
Project: 100727
Buggy source:
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes atts) throws SAXException {
  final AttributesImpl res=new AttributesImpl(atts);
  final String cls=atts.getValue(ATTRIBUTE_NAME_CLASS);
  classStack.addFirst(cls);
  if (TOPIC_TGROUP.matches(cls)) {
    if (colSpec != null) {
      colSpecStack.addFirst(colSpec);
      rowNumStack.addFirst(rowNumber);
      columnNumberStack.addFirst(columnNumber);
      columnNumberEndStack.addFirst(columnNumberEnd);
      rowsMapStack.addFirst(rowsMap);
      colSpanMapStack.addFirst(colSpanMap);
    }
    columnNumber=1;
    columnNumberEnd=0;
    rowsMap=new HashMap<String,Integer>();
    colSpanMap=new HashMap<String,Integer>();
    colSpec=new ArrayList<String>(16);
    rowNumber=0;
  }
 else   if (TOPIC_ROW.matches(cls)) {
    columnNumber=1;
    columnNumberEnd=0;
    rowNumber++;
  }
 else   if (TOPIC_COLSPEC.matches(cls)) {
    columnNumber=columnNumberEnd + 1;
    if (atts.getValue(ATTRIBUTE_NAME_COLNAME) != null) {
      colSpec.add(atts.getValue(ATTRIBUTE_NAME_COLNAME));
    }
 else {
      colSpec.add(COLUMN_NAME_COL + columnNumber);
    }
    columnNumberEnd=columnNumber;
    XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_COLNAME,COLUMN_NAME_COL + columnNumber);
    totalColumns=columnNumberEnd;
  }
 else   if (TOPIC_ENTRY.matches(cls)) {
    columnNumber=getStartNumber(atts,columnNumberEnd);
    if (columnNumber > columnNumberEnd) {
      if (rowNumber == 1) {
        XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_COLNAME,COLUMN_NAME_COL + columnNumber);
        if (atts.getValue(ATTRIBUTE_NAME_NAMEST) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEST,COLUMN_NAME_COL + columnNumber);
        }
        if (atts.getValue(ATTRIBUTE_NAME_NAMEEND) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEEND,COLUMN_NAME_COL + getEndNumber(atts,columnNumber));
        }
      }
 else {
        int offset=0;
        int currentCol=columnNumber;
        while (currentCol <= totalColumns) {
          int previous_offset=offset;
          for (int row=1; row < rowNumber; row++) {
            final String pos=Integer.toString(row) + "String_Node_Str" + Integer.toString(currentCol);
            if (rowsMap.containsKey(pos)) {
              final int totalSpanRows=rowsMap.get(pos);
              if (rowNumber <= totalSpanRows) {
                offset+=colSpanMap.get(pos);
              }
            }
          }
          if (offset > previous_offset) {
            currentCol=columnNumber + offset;
            previous_offset=offset;
          }
 else {
            break;
          }
        }
        columnNumber=columnNumber + offset;
        if (atts.getValue(ATTRIBUTE_NAME_MOREROWS) != null) {
          final String pos=Integer.toString(rowNumber) + "String_Node_Str" + Integer.toString(columnNumber);
          rowsMap.put(pos,Integer.parseInt(atts.getValue(ATTRIBUTE_NAME_MOREROWS)) + rowNumber);
          colSpanMap.put(pos,getColumnSpan(atts));
        }
        XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_COLNAME,COLUMN_NAME_COL + columnNumber);
        if (atts.getValue(ATTRIBUTE_NAME_NAMEST) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEST,COLUMN_NAME_COL + columnNumber);
        }
        if (atts.getValue(ATTRIBUTE_NAME_NAMEEND) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEEND,COLUMN_NAME_COL + getEndNumber(atts,columnNumber));
        }
      }
    }
    columnNumberEnd=getEndNumber(atts,columnNumber);
  }
 else   if (MAP_MAP.matches(cls)) {
    if (res.getIndex(ATTRIBUTE_NAME_CASCADE) == -1) {
      XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_CASCADE,configuration.containsKey("String_Node_Str") ? configuration.get("String_Node_Str") : ATTRIBUTE_CASCADE_VALUE_MERGE);
    }
  }
  if (MAP_TOPICREF.matches(cls)) {
    final String format=res.getValue(ATTRIBUTE_NAME_FORMAT);
    final String scope=res.getValue(ATTRIBUTE_NAME_SCOPE);
    final URI href=toURI(res.getValue(ATTRIBUTE_NAME_HREF));
    if (format == null && (scope == null || scope.equals(ATTR_SCOPE_VALUE_LOCAL)) && href != null) {
      final URI target=toURI(currentFile).resolve(href);
      final Job.FileInfo fi=job.getFileInfo(target);
      if (fi != null && ATTR_FORMAT_VALUE_DITAMAP.equals(fi.format)) {
        XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_FORMAT,fi.format);
      }
    }
  }
  getContentHandler().startElement(uri,localName,qName,res);
}

Fixed version (ground truth):
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes atts) throws SAXException {
  final AttributesImpl res=new AttributesImpl(atts);
  final String cls=atts.getValue(ATTRIBUTE_NAME_CLASS);
  classStack.addFirst(cls);
  if (TOPIC_TGROUP.matches(cls)) {
    if (colSpec != null) {
      colSpecStack.addFirst(colSpec);
      rowNumStack.addFirst(rowNumber);
      columnNumberStack.addFirst(columnNumber);
      columnNumberEndStack.addFirst(columnNumberEnd);
      rowsMapStack.addFirst(rowsMap);
      colSpanMapStack.addFirst(colSpanMap);
    }
    columnNumber=1;
    columnNumberEnd=0;
    rowsMap=new HashMap<String,Integer>();
    colSpanMap=new HashMap<String,Integer>();
    colSpec=new ArrayList<String>(16);
    rowNumber=0;
  }
 else   if (TOPIC_ROW.matches(cls)) {
    columnNumber=1;
    columnNumberEnd=0;
    rowNumber++;
  }
 else   if (TOPIC_COLSPEC.matches(cls)) {
    columnNumber=columnNumberEnd + 1;
    if (atts.getValue(ATTRIBUTE_NAME_COLNAME) != null) {
      colSpec.add(atts.getValue(ATTRIBUTE_NAME_COLNAME));
    }
 else {
      colSpec.add(COLUMN_NAME_COL + columnNumber);
    }
    columnNumberEnd=columnNumber;
    XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_COLNAME,COLUMN_NAME_COL + columnNumber);
    totalColumns=columnNumberEnd;
  }
 else   if (TOPIC_ENTRY.matches(cls)) {
    columnNumber=getStartNumber(atts,columnNumberEnd);
    if (columnNumber > columnNumberEnd) {
      if (rowNumber == 1) {
        XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_COLNAME,COLUMN_NAME_COL + columnNumber);
        if (atts.getValue(ATTRIBUTE_NAME_NAMEST) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEST,COLUMN_NAME_COL + columnNumber);
        }
        if (atts.getValue(ATTRIBUTE_NAME_NAMEEND) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEEND,COLUMN_NAME_COL + getEndNumber(atts,columnNumber));
        }
      }
 else {
        int offset=0;
        int currentCol=columnNumber;
        while (currentCol <= totalColumns) {
          int previous_offset=offset;
          for (int row=1; row < rowNumber; row++) {
            final String pos=Integer.toString(row) + "String_Node_Str" + Integer.toString(currentCol);
            if (rowsMap.containsKey(pos)) {
              final int totalSpanRows=rowsMap.get(pos);
              if (rowNumber <= totalSpanRows) {
                offset+=colSpanMap.get(pos);
              }
            }
          }
          if (offset > previous_offset) {
            currentCol=columnNumber + offset;
            previous_offset=offset;
          }
 else {
            break;
          }
        }
        columnNumber=columnNumber + offset;
        if (atts.getValue(ATTRIBUTE_NAME_MOREROWS) != null) {
          final String pos=Integer.toString(rowNumber) + "String_Node_Str" + Integer.toString(columnNumber);
          rowsMap.put(pos,Integer.parseInt(atts.getValue(ATTRIBUTE_NAME_MOREROWS)) + rowNumber);
          colSpanMap.put(pos,getColumnSpan(atts));
        }
        XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_COLNAME,COLUMN_NAME_COL + columnNumber);
        if (atts.getValue(ATTRIBUTE_NAME_NAMEST) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEST,COLUMN_NAME_COL + columnNumber);
        }
        if (atts.getValue(ATTRIBUTE_NAME_NAMEEND) != null) {
          XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_NAMEEND,COLUMN_NAME_COL + getEndNumber(atts,columnNumber));
        }
      }
    }
    columnNumberEnd=getEndNumber(atts,columnNumber);
  }
 else   if (MAP_MAP.matches(cls)) {
    if (res.getIndex(ATTRIBUTE_NAME_CASCADE) == -1) {
      XMLUtils.addOrSetAttribute(res,ATTRIBUTE_NAME_CASCADE,configuration.containsKey("String_Node_Str") ? configuration.get("String_Node_Str") : ATTRIBUTE_CASCADE_VALUE_MERGE);
    }
  }
  getContentHandler().startElement(uri,localName,qName,res);
}