56 0 obj
    << /Length 1242 /Filter /FlateDecode >>
    stream
    x]êΩnƒ Ñ{ûbÀKq¬æâê¢....(whole binary is omitted)
    endstream
    endobj

qpdf --qdf in.pdf out.pdf

header('Content-Type: text'); // I going to download the result of decoding
$n = "binary_file.bin"; // decoded part in file in a directory
$f = @fopen($n, "rb"); // now file is mine
$c = fread($f, filesize($n)); // now I know all about it
$u = @gzuncompress($c); // function, exactly fits for this /FlateDecode filter
$out = fopen("php://output", "wb"); // ready to output anywhere
fwrite($out, $u);// output to downloadable file

FlateFilter filter = new FlateFilter(null);
byte[] decoded = filter.decode(bytes, start, end - start);