Program: 30640
Project: 30640
Buggy source:
private void parseBarcodeFile(final ArrayList<String> messages){
  final TabbedTextFileWithHeaderParser barcodesParser=new TabbedTextFileWithHeaderParser(BARCODE_FILE);
  final String sequenceColumn=barcodesParser.hasColumn(BARCODE_SEQUENCE_COLUMN) ? BARCODE_SEQUENCE_COLUMN : barcodesParser.hasColumn(BARCODE_SEQUENCE_1_COLUMN) ? BARCODE_SEQUENCE_1_COLUMN : null;
  if (sequenceColumn == null) {
    messages.add(BARCODE_FILE + "String_Node_Str" + BARCODE_SEQUENCE_COLUMN+ "String_Node_Str"+ BARCODE_SEQUENCE_1_COLUMN+ "String_Node_Str");
    return;
  }
  final boolean hasBarcodeName=barcodesParser.hasColumn(BARCODE_NAME_COLUMN);
  final boolean hasLibraryName=barcodesParser.hasColumn(LIBRARY_NAME_COLUMN);
  final int numBarcodes=readStructure.barcodeIndices.length;
  final Set<String> barcodes=new HashSet<String>();
  for (  final TabbedTextFileWithHeaderParser.Row row : barcodesParser) {
    final String bcStrings[]=new String[numBarcodes];
    int barcodeNum=1;
    for (    final ReadDescriptor rd : readStructure.descriptors) {
      if (rd.type != ReadType.Barcode)       continue;
      final String header=barcodeNum == 1 ? sequenceColumn : "String_Node_Str" + String.valueOf(barcodeNum);
      bcStrings[barcodeNum - 1]=row.getField(header);
      barcodeNum++;
    }
    final String bcStr=barcodeSeqsToString(bcStrings,barcodeDelimiter);
    if (barcodes.contains(bcStr)) {
      messages.add("String_Node_Str" + bcStr + "String_Node_Str"+ BARCODE_FILE);
    }
    barcodes.add(bcStr);
    final String barcodeName=(hasBarcodeName ? row.getField(BARCODE_NAME_COLUMN) : "String_Node_Str");
    final String libraryName=(hasLibraryName ? row.getField(LIBRARY_NAME_COLUMN) : "String_Node_Str");
    final BarcodeMetric metric=new BarcodeMetric(barcodeName,libraryName,bcStr,bcStrings);
    barcodeMetrics.add(metric);
  }
}

Fixed version (ground truth):
private void parseBarcodeFile(final ArrayList<String> messages){
  final TabbedTextFileWithHeaderParser barcodesParser=new TabbedTextFileWithHeaderParser(BARCODE_FILE);
  final String sequenceColumn=barcodesParser.hasColumn(BARCODE_SEQUENCE_COLUMN) ? BARCODE_SEQUENCE_COLUMN : barcodesParser.hasColumn(BARCODE_SEQUENCE_1_COLUMN) ? BARCODE_SEQUENCE_1_COLUMN : null;
  if (sequenceColumn == null) {
    messages.add(BARCODE_FILE + "String_Node_Str" + BARCODE_SEQUENCE_COLUMN+ "String_Node_Str"+ BARCODE_SEQUENCE_1_COLUMN+ "String_Node_Str");
    return;
  }
  final boolean hasBarcodeName=barcodesParser.hasColumn(BARCODE_NAME_COLUMN);
  final boolean hasLibraryName=barcodesParser.hasColumn(LIBRARY_NAME_COLUMN);
  final int numBarcodes=readStructure.barcodeIndices.length;
  final Set<String> barcodes=new HashSet<String>();
  for (  final TabbedTextFileWithHeaderParser.Row row : barcodesParser) {
    final String bcStrings[]=new String[numBarcodes];
    int barcodeNum=1;
    for (    final ReadDescriptor rd : readStructure.descriptors) {
      if (rd.type != ReadType.Barcode)       continue;
      final String header=barcodeNum == 1 ? sequenceColumn : "String_Node_Str" + String.valueOf(barcodeNum);
      bcStrings[barcodeNum - 1]=row.getField(header);
      barcodeNum++;
    }
    final String bcStr=barcodeSeqsToString(bcStrings,barcodeDelimiter);
    if (barcodes.contains(bcStr)) {
      messages.add("String_Node_Str" + bcStr + "String_Node_Str"+ BARCODE_FILE);
    }
    barcodes.add(bcStr);
    final String barcodeName=(hasBarcodeName ? row.getField(BARCODE_NAME_COLUMN) : "String_Node_Str");
    final String libraryName=(hasLibraryName ? row.getField(LIBRARY_NAME_COLUMN) : "String_Node_Str");
    final BarcodeMetric metric=new BarcodeMetric(barcodeName,libraryName,bcStr,bcStrings);
    barcodeMetrics.add(metric);
  }
  barcodesParser.close();
}