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<?php class AnyWay_PhpEmbeddedFsArchive extends AnyWay_PhpEmbeddedFs { // https://sourceforge.net/p/picard/code/HEAD/tree/trunk/src/java/net/sf/samtools/util/BlockCompressedStreamConstants.java#l55 // DONT EVER TRY TO CHANGE DEFAULT_UNCOMPRESSED_BLOCK_SIZE TO 65536 OR SOMETHING NOT DIVIDING TO 512 // AS DECOMPRESS CANNOT HANDLE THAT const DEFAULT_UNCOMPRESSED_BLOCK_SIZE = 65024; // http://sourceforge.net/p/samtools/mailman/message/29894810/ // it used to be 65536, but $bsize = pack("v", strlen($compressed) + 25); so it must be 25 bytes shorter or else an overflow might happen // however DEFAULT_UNCOMPRESSED_BLOCK_SIZE = 65024 produces 65034 bytes at most const DEFAULT_COMPRESSED_BLOCK_SIZE = 65510; protected static $_magic = "\x1f\x8b\x08\x04"; protected static $_header = "\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00BC\x02\x00"; protected static $_eof = "\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00BC\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00"; protected $_buffer = ''; public function __construct($filename) { parent::__construct($filename); $this->_buffer = ''; } public function fopen($filename, $mode) { throw new Exception("Use gzopen instead"); } public function fwrite($handle, $data, $length = null) { throw new Exception("Use gzwrite instead"); } public function fseek($handle, $offset, $mode = SEEK_SET) { throw new Exception("Use gzseek instead"); } public function ftell($handle) { throw new Exception("Use gztell instead"); } public function fread($handle, $length) { throw new Exception("Use gzreadblock instead"); } public function fclose($handle, $write_fat = true) { throw new Exception("Use gzclose instead"); } public function fflush($handle) { throw new Exception("Use gzflush instead"); } public function gzopen($filename, $mode) { return parent::fopen($filename, $mode); } private function _write_block($handle, $block) { $blocklen = strlen($block); // this is redundant, in case if ($blocklen > self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE) throw new Exception("Unable to handle blocks larger than " . self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE); $compressed = gzdeflate($block, 9); if (strlen($compressed) >= self::DEFAULT_COMPRESSED_BLOCK_SIZE) { //throw new Exception("TODO - Didn't compress enough, try less data in this block"); $chunks = str_split($block, self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE - 1024); $result = 0; foreach ($chunks as $chunk) { $result += $this->_write_block($handle, $chunk); } return $result; } // https://github.com/attractivechaos/klib/blob/master/bgzf.c // compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; 18 + 8 $bsize = pack("v", strlen($compressed) + 25); // unsigned short 2 bytes $crc = pack("V", crc32($block)); // unsigned int 4 bytes $uncompressed_length = pack("V", strlen($block)); // unsigned int 4 bytes /* # Fixed 16 bytes, # gzip magic bytes (4) mod time (4), # gzip flag (1), os (1), extra length which is six (2), # sub field which is BC (2), sub field length of two (2), # "\x1f\x8b\x08\x04" # "\x00"\x00\x00\x00" mod time # "\x00" gzip flag # "\xff" os # "\x06\x00" extra length # "\x42\x43" BC # "\x02\x00" subfield length; # Variable data, # 2 bytes: block length as BC sub field (2) # X bytes: the data # 8 bytes: crc (4), uncompressed data length (4) / $data = self::$_header . $bsize . $compressed . $crc . $uncompressed_length; $result = parent::fwrite($handle, $data); // for tests only if (isset($GLOBALS["anyway_iosleep"])) usleep($GLOBALS["anyway_iosleep"] 1000000); return $result; } public function gzwrite($handle, $data) { $this->_buffer .= $data; while (strlen($this->_buffer) >= self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE) { $this->_write_block($handle, substr($this->_buffer, 0, self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE)); $this->_buffer = substr($this->_buffer, self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE); } return strlen($data); } public function gzflush($handle) { while (strlen($this->_buffer)) { $this->_write_block($handle, substr($this->_buffer, 0, self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE)); $this->_buffer = substr($this->_buffer, self::DEFAULT_UNCOMPRESSED_BLOCK_SIZE); } return true; } public function gzclose($handle, $writeEof = false) { if ($this->fh_appending === $handle) { $this->gzflush($handle); if ($writeEof) { parent::fwrite($handle, self::$_eof); } fseek($handle, 0, SEEK_END); $position = parent::ftell($handle); $result = parent::fclose($handle); return $result ? $position : false; } return parent::fclose($handle); } public function gzseek($handle, $offset, $mode = SEEK_SET) { return parent::fseek($handle, $offset, $mode); } public function gztell($handle) { return parent::ftell($handle); } public function gzreadblock($handle) { if (false === ($_magic = parent::fread($handle, 4))) return false; if ($_magic != self::$_magic) throw new Exception("Magic header not found"); $_header = parent::fread($handle, 8); $t = unpack("Vgzip_mod_time/Cgzip_extra_flags/Cgzip_os/vextra_len", $_header); $extra_len = $t['extra_len']; $block_size = null; $x_len = 0; while ($x_len < $extra_len) { $_subfield_id = parent::fread($handle, 2); $_subfield_len = parent::fread($handle, 2); $t = unpack("vsubfield_len", $_subfield_len); $_subfield = parent::fread($handle, $t['subfield_len']); $x_len += $t['subfield_len'] + 4; if ($_subfield_id === "BC") { if ($t['subfield_len'] !== 2) throw new Exception("Wrong BC payload length"); if ($block_size !== null) throw new Exception("Two BC subfields?"); $t = unpack("vblock_size", $_subfield); $block_size = $t['block_size']; } } /* # Fixed 16 bytes, # "\x1f\x8b\x08\x04" # "\x00"\x00\x00\x00" mod time # "\x00" gzip flag # "\xff" os # "\x06\x00" extra length <-- $_header # "\x42\x43" BC <-- $_subfield_id # "\x02\x00" subfield length; <-- $_subfield_len # Variable data, # 2 bytes: block length as BC sub field (2) <- $block_size # X bytes: the data # 8 bytes: crc (4), uncompressed data length (4) / if ($x_len !== $extra_len) throw new Exception(sprintf("Extra len %d, not %d", $x_len, $extra_len)); if ($block_size === null) throw new Exception("Missing BC, this isn't a BGZF file!"); $deflate_size = $block_size - 25; $_data = parent::fread($handle, $deflate_size); $data = gzinflate($_data); $_expected_crc = parent::fread($handle, 4); $_expected_size = parent::fread($handle, 4); $t = unpack("Vexpected_size", $_expected_size); if ($t['expected_size'] !== strlen($data)) { $block = join('-', array( bin2hex($_magic), bin2hex($_header), bin2hex($_subfield_id), bin2hex($_subfield_len), bin2hex($_subfield), strlen($_data), bin2hex($_expected_crc), bin2hex($_expected_size) )); throw new Exception(sprintf("Decompressed to '%s', not '%s', block '%s' at position %d", strlen($data), $t['expected_size'], $block, parent::ftell($handle))); } $crc = pack("V", crc32($data)); if ($_expected_crc !== $crc) throw new Exception(sprintf("CRC is %s, not %s", $crc, $_expected_crc)); // for tests only if (isset($GLOBALS["anyway_iosleep"])) usleep($GLOBALS["anyway_iosleep"] 1000000); return $data; } public function close() { if (is_resource($this->fh)) { if ($this->opened_for_write) { while ($this->FAT_fhlookup) { $handle = reset($this->FAT_fhlookup); if (false === $this->gzclose($handle)) throw new Exception("Unable to close handle"); } // this will be flushed in parent::close(); // $this->_write_fat(); } parent::close(); } } }

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