Program: 33363
Project: 33363
Buggy source:
public static void main(String[] args) throws Exception {
  RandomAccessInputStream rin=new FileCacheRandomAccessInputStream(new FileInputStream(args[0]));
  RandomAccessOutputStream rout=null;
  if (args.length > 1) {
    if (args[1].equalsIgnoreCase("String_Node_Str")) {
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      TIFFTweaker.copyCat(rin,rout);
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      TIFFTweaker.snoop(rin);
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      int pageCount=TIFFTweaker.getPageCount(rin);
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      if (pageCount > 1)       TIFFTweaker.retainPages(rin,rout,pageCount - 1);
 else       TIFFTweaker.copyCat(rin,rout);
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str") || args[1].equalsIgnoreCase("String_Node_Str")) {
      File[] files=FileUtils.listFilesMatching(new File(args[2]),args[3]);
      TIFFFrame[] frames=new TIFFFrame[files.length];
      for (int i=0; i < files.length; i++) {
        FileInputStream fin=new FileInputStream(files[i]);
        BufferedImage image=javax.imageio.ImageIO.read(fin);
        frames[i]=new TIFFFrame(image);
        fin.close();
      }
      ImageMeta.ImageMetaBuilder builder=new ImageMeta.ImageMetaBuilder();
      TIFFOptions tiffOptions=new TIFFOptions();
      tiffOptions.setTiffCompression(Compression.LZW);
      tiffOptions.setApplyPredictor(true);
      tiffOptions.setDeflateCompressionLevel(6);
      builder.imageOptions(tiffOptions);
      frames[0].setFrameMeta(builder.grayscale(true).applyDither(true).ditherThreshold(18).hasAlpha(true).build());
      tiffOptions=new TIFFOptions(tiffOptions);
      tiffOptions.setTiffCompression(Compression.DEFLATE);
      frames[1].setFrameMeta(builder.imageOptions(tiffOptions).build());
      tiffOptions=new TIFFOptions(tiffOptions);
      tiffOptions.setTiffCompression(Compression.CCITTFAX4);
      ImageMeta meta=builder.bilevel(true).imageOptions(tiffOptions).build();
      for (int i=2; i < frames.length; i++)       frames[i].setFrameMeta(meta);
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      if (args[1].equalsIgnoreCase("String_Node_Str"))       TIFFTweaker.writeMultipageTIFF(rout,frames);
 else {
        long t1=System.currentTimeMillis();
        List<IFD> list=new ArrayList<IFD>();
        int offset=TIFFTweaker.prepareForInsert(rin,rout,list);
        int index=3;
        TIFFWriter writer=new TIFFWriter();
        writer.setImageMeta(frames[0].getFrameMeta());
        for (int i=0; i < frames.length; i++) {
          offset=TIFFTweaker.insertPage(frames[i].getFrame(),index+=2,rout,list,offset,writer);
        }
        int nColors=2;
        byte[] reds=new byte[]{0,(byte)255};
        byte[] greens=new byte[]{0,(byte)255};
        byte[] blues=new byte[]{0,(byte)255};
        int width=400;
        int height=400;
        IndexColorModel colorModel=new IndexColorModel(1,nColors,reds,greens,blues);
        BufferedImage im=new BufferedImage(width,height,BufferedImage.TYPE_BYTE_BINARY,colorModel);
        WritableRaster raster=im.getRaster();
        for (int h=0; h < height; h++)         for (int w=0; w < width; w++)         if (((h / 50) + (w / 50)) % 2 == 0)         raster.setSample(w,h,0,0);
 else         raster.setSample(w,h,0,1);
        writer.setImageMeta(frames[2].getFrameMeta());
        TIFFTweaker.insertPage(im,0,rout,list,offset,writer);
        TIFFTweaker.finishInsert(rout,list);
        long t2=System.currentTimeMillis();
        System.out.println("String_Node_Str" + (t2 - t1) + "String_Node_Str");
      }
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      TIFFTweaker.splitPages(rin,FileUtils.getNameWithoutExtension(new File(args[0])));
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      TIFFTweaker.insertExif(rin,rout,populateExif());
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      int pageCount=TIFFTweaker.getPageCount(rin);
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      if (pageCount > 1)       TIFFTweaker.removePages(rin,rout,0,2,4,100,-100);
 else       TIFFTweaker.copyCat(rin,rout);
      rout.close();
    }
  }
  rin.close();
}

Fixed version (ground truth):
public static void main(String[] args) throws Exception {
  RandomAccessInputStream rin=new FileCacheRandomAccessInputStream(new FileInputStream(args[0]));
  RandomAccessOutputStream rout=null;
  if (args.length > 1) {
    if (args[1].equalsIgnoreCase("String_Node_Str")) {
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      TIFFTweaker.copyCat(rin,rout);
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      TIFFTweaker.snoop(rin);
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      int pageCount=TIFFTweaker.getPageCount(rin);
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      if (pageCount > 1)       TIFFTweaker.retainPages(rin,rout,pageCount - 1);
 else       TIFFTweaker.copyCat(rin,rout);
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str") || args[1].equalsIgnoreCase("String_Node_Str")) {
      File[] files=FileUtils.listFilesMatching(new File(args[2]),args[3]);
      TIFFFrame[] frames=new TIFFFrame[files.length];
      for (int i=0; i < files.length; i++) {
        FileInputStream fin=new FileInputStream(files[i]);
        BufferedImage image=javax.imageio.ImageIO.read(fin);
        frames[i]=new TIFFFrame(image);
        fin.close();
      }
      ImageMeta.ImageMetaBuilder builder=new ImageMeta.ImageMetaBuilder();
      TIFFOptions tiffOptions=new TIFFOptions();
      tiffOptions.setTiffCompression(Compression.LZW);
      tiffOptions.setApplyPredictor(true);
      tiffOptions.setDeflateCompressionLevel(6);
      builder.imageOptions(tiffOptions);
      frames[0].setFrameMeta(builder.grayscale(true).applyDither(true).ditherThreshold(18).hasAlpha(true).build());
      tiffOptions=new TIFFOptions(tiffOptions);
      tiffOptions.setTiffCompression(Compression.DEFLATE);
      frames[1].setFrameMeta(builder.imageOptions(tiffOptions).build());
      tiffOptions=new TIFFOptions(tiffOptions);
      tiffOptions.setTiffCompression(Compression.CCITTFAX4);
      ImageMeta meta=builder.bilevel(true).imageOptions(tiffOptions).build();
      for (int i=2; i < frames.length; i++)       frames[i].setFrameMeta(meta);
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      if (args[1].equalsIgnoreCase("String_Node_Str"))       TIFFTweaker.writeMultipageTIFF(rout,frames);
 else {
        long t1=System.currentTimeMillis();
        List<IFD> list=new ArrayList<IFD>();
        int offset=TIFFTweaker.prepareForInsert(rin,rout,list);
        int index=3;
        TIFFWriter writer=new TIFFWriter();
        writer.setImageMeta(frames[0].getFrameMeta());
        for (int i=0; i < frames.length; i++) {
          offset=TIFFTweaker.insertPage(frames[i].getFrame(),index+=2,rout,list,offset,writer);
        }
        int nColors=2;
        byte[] reds=new byte[]{0,(byte)255};
        byte[] greens=new byte[]{0,(byte)255};
        byte[] blues=new byte[]{0,(byte)255};
        int width=400;
        int height=400;
        IndexColorModel colorModel=new IndexColorModel(1,nColors,reds,greens,blues);
        BufferedImage im=new BufferedImage(width,height,BufferedImage.TYPE_BYTE_BINARY,colorModel);
        WritableRaster raster=im.getRaster();
        for (int h=0; h < height; h++)         for (int w=0; w < width; w++)         if (((h / 50) + (w / 50)) % 2 == 0)         raster.setSample(w,h,0,0);
 else         raster.setSample(w,h,0,1);
        writer.setImageMeta(frames[2].getFrameMeta());
        TIFFTweaker.insertPage(im,0,rout,list,offset,writer);
        TIFFTweaker.finishInsert(rout,list);
        long t2=System.currentTimeMillis();
        System.out.println("String_Node_Str" + (t2 - t1) + "String_Node_Str");
      }
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      TIFFTweaker.splitPages(rin,FileUtils.getNameWithoutExtension(new File(args[0])));
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      TIFFTweaker.insertExif(rin,rout,populateExif());
      rout.close();
    }
 else     if (args[1].equalsIgnoreCase("String_Node_Str")) {
      int pageCount=TIFFTweaker.getPageCount(rin);
      rout=new FileCacheRandomAccessOutputStream(new FileOutputStream("String_Node_Str"));
      if (pageCount > 1)       TIFFTweaker.removePages(rin,rout,0,1,1,1,5,5,4,100,-100);
 else       TIFFTweaker.copyCat(rin,rout);
      rout.close();
    }
  }
  rin.close();
}