src/api/internal/io/BgzfStream_p.cpp

   1 // ***************************************************************************
   2 // BgzfStream_p.cpp (c) 2011 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 17 January 2012(DB)
   6 // ---------------------------------------------------------------------------
   7 // Based on BGZF routines developed at the Broad Institute.
   8 // Provides the basic functionality for reading & writing BGZF files
   9 // Replaces the old BGZF.* files to avoid clashing with other toolkits
  10 // ***************************************************************************
  11
  12 #include "api/BamAux.h"
  13 #include "api/BamConstants.h"
  14 #include "api/internal/io/BamDeviceFactory_p.h"
  15 #include "api/internal/io/BgzfStream_p.h"
  16 #include "api/internal/utils/BamException_p.h"
  17 using namespace BamTools;
  18 using namespace BamTools::Internal;
  19
  20 #include "zlib.h"
  21
  22 #include <cstring>
  23 #include <algorithm>
  24 #include <iostream>
  25 #include <sstream>
  26 using namespace std;
  27
  28 // ---------------------------
  29 // BgzfStream implementation
  30 // ---------------------------
  31
  32 // constructor
  33 BgzfStream::BgzfStream(void)
  34   : m_blockLength(0)
  35   , m_blockOffset(0)
  36   , m_blockAddress(0)
  37   , m_isWriteCompressed(true)
  38   , m_device(0)
  39   , m_uncompressedBlock(Constants::BGZF_DEFAULT_BLOCK_SIZE)
  40   , m_compressedBlock(Constants::BGZF_MAX_BLOCK_SIZE)
  41 { }
  42
  43 // destructor
  44 BgzfStream::~BgzfStream(void) {
  45     Close();
  46 }
  47
  48 // checks BGZF block header
  49 bool BgzfStream::CheckBlockHeader(char* header) {
  50     return (header[0] == Constants::GZIP_ID1 &&
  51             header[1] == Constants::GZIP_ID2 &&
  52             header[2] == Z_DEFLATED &&
  53             (header[3] & Constants::FLG_FEXTRA) != 0 &&
  54             BamTools::UnpackUnsignedShort(&header[10]) == Constants::BGZF_XLEN &&
  55             header[12] == Constants::BGZF_ID1 &&
  56             header[13] == Constants::BGZF_ID2 &&
  57             BamTools::UnpackUnsignedShort(&header[14]) == Constants::BGZF_LEN );
  58 }
  59
  60 // closes BGZF file
  61 void BgzfStream::Close(void) {
  62
  63     // skip if no device open
  64     if ( m_device == 0 ) return;
  65
  66     // if writing to file, flush the current BGZF block,
  67     // then write an empty block (as EOF marker)
  68     if ( m_device->IsOpen() && (m_device->Mode() == IBamIODevice::WriteOnly) ) {
  69         FlushBlock();
  70         const size_t blockLength = DeflateBlock(0);
  71         m_device->Write(m_compressedBlock.Buffer, blockLength);
  72     }
  73
  74     // close device
  75     m_device->Close();
  76     delete m_device;
  77     m_device = 0;
  78
  79     // ensure our buffers are cleared out
  80     m_uncompressedBlock.Clear();
  81     m_compressedBlock.Clear();
  82
  83     // reset state
  84     m_blockLength = 0;
  85     m_blockOffset = 0;
  86     m_blockAddress = 0;
  87     m_isWriteCompressed = true;
  88 }
  89
  90 // compresses the current block
  91 size_t BgzfStream::DeflateBlock(int32_t blockLength) {
  92
  93     // initialize the gzip header
  94     char* buffer = m_compressedBlock.Buffer;
  95     memset(buffer, 0, 18);
  96     buffer[0]  = Constants::GZIP_ID1;
  97     buffer[1]  = Constants::GZIP_ID2;
  98     buffer[2]  = Constants::CM_DEFLATE;
  99     buffer[3]  = Constants::FLG_FEXTRA;
 100     buffer[9]  = Constants::OS_UNKNOWN;
 101     buffer[10] = Constants::BGZF_XLEN;
 102     buffer[12] = Constants::BGZF_ID1;
 103     buffer[13] = Constants::BGZF_ID2;
 104     buffer[14] = Constants::BGZF_LEN;
 105
 106     // set compression level
 107     const int compressionLevel = ( m_isWriteCompressed ? Z_DEFAULT_COMPRESSION : 0 );
 108
 109     // loop to retry for blocks that do not compress enough
 110     int inputLength = blockLength;
 111     size_t compressedLength = 0;
 112     const unsigned int bufferSize = Constants::BGZF_MAX_BLOCK_SIZE;
 113
 114     while ( true ) {
 115
 116         // initialize zstream values
 117         z_stream zs;
 118         zs.zalloc    = NULL;
 119         zs.zfree     = NULL;
 120         zs.next_in   = (Bytef*)m_uncompressedBlock.Buffer;
 121         zs.avail_in  = inputLength;
 122         zs.next_out  = (Bytef*)&buffer[Constants::BGZF_BLOCK_HEADER_LENGTH];
 123         zs.avail_out = bufferSize -
 124                        Constants::BGZF_BLOCK_HEADER_LENGTH -
 125                        Constants::BGZF_BLOCK_FOOTER_LENGTH;
 126
 127         // initialize the zlib compression algorithm
 128         int status = deflateInit2(&zs,
 129                                   compressionLevel,
 130                                   Z_DEFLATED,
 131                                   Constants::GZIP_WINDOW_BITS,
 132                                   Constants::Z_DEFAULT_MEM_LEVEL,
 133                                   Z_DEFAULT_STRATEGY);
 134         if ( status != Z_OK )
 135             throw BamException("BgzfStream::DeflateBlock", "zlib deflateInit2 failed");
 136
 137         // compress the data
 138         status = deflate(&zs, Z_FINISH);
 139
 140         // if not at stream end
 141         if ( status != Z_STREAM_END ) {
 142
 143             deflateEnd(&zs);
 144
 145             // there was not enough space available in buffer
 146             // try to reduce the input length & re-start loop
 147             if ( status == Z_OK ) {
 148                 inputLength -= 1024;
 149                 if ( inputLength < 0 )
 150                     throw BamException("BgzfStream::DeflateBlock", "input reduction failed");
 151                 continue;
 152             }
 153
 154             throw BamException("BgzfStream::DeflateBlock", "zlib deflate failed");
 155         }
 156
 157         // finalize the compression routine
 158         status = deflateEnd(&zs);
 159         if ( status != Z_OK )
 160             throw BamException("BgzfStream::DeflateBlock", "zlib deflateEnd failed");
 161
 162         // update compressedLength
 163         compressedLength = zs.total_out +
 164                            Constants::BGZF_BLOCK_HEADER_LENGTH +
 165                            Constants::BGZF_BLOCK_FOOTER_LENGTH;
 166         if ( compressedLength > Constants::BGZF_MAX_BLOCK_SIZE )
 167             throw BamException("BgzfStream::DeflateBlock", "deflate overflow");
 168
 169         // quit while loop
 170         break;
 171     }
 172
 173     // store the compressed length
 174     BamTools::PackUnsignedShort(&buffer[16], static_cast<uint16_t>(compressedLength - 1));
 175
 176     // store the CRC32 checksum
 177     uint32_t crc = crc32(0, NULL, 0);
 178     crc = crc32(crc, (Bytef*)m_uncompressedBlock.Buffer, inputLength);
 179     BamTools::PackUnsignedInt(&buffer[compressedLength - 8], crc);
 180     BamTools::PackUnsignedInt(&buffer[compressedLength - 4], inputLength);
 181
 182     // ensure that we have less than a block of data left
 183     int remaining = blockLength - inputLength;
 184     if ( remaining > 0 ) {
 185         if ( remaining > inputLength )
 186             throw BamException("BgzfStream::DeflateBlock", "after deflate, remainder too large");
 187         memcpy(m_uncompressedBlock.Buffer, m_uncompressedBlock.Buffer + inputLength, remaining);
 188     }
 189
 190     // update block data
 191     m_blockOffset = remaining;
 192
 193     // return result
 194     return compressedLength;
 195 }
 196
 197 // flushes the data in the BGZF block
 198 void BgzfStream::FlushBlock(void) {
 199
 200     BT_ASSERT_X( m_device, "BgzfStream::FlushBlock() - attempting to flush to null device" );
 201
 202     // flush all of the remaining blocks
 203     while ( m_blockOffset > 0 ) {
 204
 205         // compress the data block
 206         const size_t blockLength = DeflateBlock(m_blockOffset);
 207
 208         // flush the data to our output device
 209         const int64_t numBytesWritten = m_device->Write(m_compressedBlock.Buffer, blockLength);
 210
 211         // check for device error
 212         if ( numBytesWritten < 0 ) {
 213             const string message = string("device error: ") + m_device->GetErrorString();
 214             throw BamException("BgzfStream::FlushBlock", message);
 215         }
 216
 217         // check that we wrote expected numBytes
 218         if ( numBytesWritten != static_cast<int64_t>(blockLength) ) {
 219             stringstream s("");
 220             s << "expected to write " << blockLength
 221               << " bytes during flushing, but wrote " << numBytesWritten;
 222             throw BamException("BgzfStream::FlushBlock", s.str());
 223         }
 224
 225         // update block data
 226         m_blockAddress += blockLength;
 227     }
 228 }
 229
 230 // decompresses the current block
 231 size_t BgzfStream::InflateBlock(const size_t& blockLength) {
 232
 233     // setup zlib stream object
 234     z_stream zs;
 235     zs.zalloc    = NULL;
 236     zs.zfree     = NULL;
 237     zs.next_in   = (Bytef*)m_compressedBlock.Buffer + 18;
 238     zs.avail_in  = blockLength - 16;
 239     zs.next_out  = (Bytef*)m_uncompressedBlock.Buffer;
 240     zs.avail_out = Constants::BGZF_DEFAULT_BLOCK_SIZE;
 241
 242     // initialize
 243     int status = inflateInit2(&zs, Constants::GZIP_WINDOW_BITS);
 244     if ( status != Z_OK )
 245         throw BamException("BgzfStream::InflateBlock", "zlib inflateInit failed");
 246
 247     // decompress
 248     status = inflate(&zs, Z_FINISH);
 249     if ( status != Z_STREAM_END ) {
 250         inflateEnd(&zs);
 251         throw BamException("BgzfStream::InflateBlock", "zlib inflate failed");
 252     }
 253
 254     // finalize
 255     status = inflateEnd(&zs);
 256     if ( status != Z_OK ) {
 257         inflateEnd(&zs);
 258         throw BamException("BgzfStream::InflateBlock", "zlib inflateEnd failed");
 259     }
 260
 261     // return result
 262     return zs.total_out;
 263 }
 264
 265 bool BgzfStream::IsOpen(void) const {
 266     if ( m_device == 0 )
 267         return false;
 268     return m_device->IsOpen();
 269 }
 270
 271 void BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode) {
 272
 273     // close current device if necessary
 274     Close();
 275     BT_ASSERT_X( (m_device == 0), "BgzfStream::Open() - unable to properly close previous IO device" );
 276
 277     // retrieve new IO device depending on filename
 278     m_device = BamDeviceFactory::CreateDevice(filename);
 279     BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from filename" );
 280
 281     // if device fails to open
 282     if ( !m_device->Open(mode) ) {
 283         const string deviceError = m_device->GetErrorString();
 284         const string message = string("could not open BGZF stream: \n\t") + deviceError;
 285         throw BamException("BgzfStream::Open", message);
 286     }
 287 }
 288
 289 // reads BGZF data into a byte buffer
 290 size_t BgzfStream::Read(char* data, const size_t dataLength) {
 291
 292     if ( dataLength == 0 )
 293         return 0;
 294
 295     // if stream not open for reading
 296     BT_ASSERT_X( m_device, "BgzfStream::Read() - trying to read from null device");
 297     if ( !m_device->IsOpen() || (m_device->Mode() != IBamIODevice::ReadOnly) )
 298         return 0;
 299
 300     // read blocks as needed until desired data length is retrieved
 301     char* output = data;
 302     size_t numBytesRead = 0;
 303     while ( numBytesRead < dataLength ) {
 304
 305         // determine bytes available in current block
 306         int bytesAvailable = m_blockLength - m_blockOffset;
 307
 308         // read (and decompress) next block if needed
 309         if ( bytesAvailable <= 0 ) {
 310             ReadBlock();
 311             bytesAvailable = m_blockLength - m_blockOffset;
 312             if ( bytesAvailable <= 0 )
 313                 break;
 314         }
 315
 316         // copy data from uncompressed source buffer into data destination buffer
 317         const size_t copyLength = min( (dataLength-numBytesRead), (size_t)bytesAvailable );
 318         memcpy(output, m_uncompressedBlock.Buffer + m_blockOffset, copyLength);
 319
 320         // update counters
 321         m_blockOffset += copyLength;
 322         output        += copyLength;
 323         numBytesRead  += copyLength;
 324     }
 325
 326     // update block data
 327     if ( m_blockOffset == m_blockLength ) {
 328         m_blockAddress = m_device->Tell();
 329         m_blockOffset  = 0;
 330         m_blockLength  = 0;
 331     }
 332
 333     // return actual number of bytes read
 334     return numBytesRead;
 335 }
 336
 337 // reads a BGZF block
 338 void BgzfStream::ReadBlock(void) {
 339
 340     BT_ASSERT_X( m_device, "BgzfStream::ReadBlock() - trying to read from null IO device");
 341
 342     // store block's starting address
 343     const int64_t blockAddress = m_device->Tell();
 344
 345     // read block header from file
 346     char header[Constants::BGZF_BLOCK_HEADER_LENGTH];
 347     int64_t numBytesRead = m_device->Read(header, Constants::BGZF_BLOCK_HEADER_LENGTH);
 348
 349     // check for device error
 350     if ( numBytesRead < 0 ) {
 351         const string message = string("device error: ") + m_device->GetErrorString();
 352         throw BamException("BgzfStream::ReadBlock", message);
 353     }
 354
 355     // if block header empty
 356     if ( numBytesRead == 0 ) {
 357         m_blockLength = 0;
 358         return;
 359     }
 360
 361     // if block header invalid size
 362     if ( numBytesRead != static_cast<int8_t>(Constants::BGZF_BLOCK_HEADER_LENGTH) )
 363         throw BamException("BgzfStream::ReadBlock", "invalid block header size");
 364
 365     // validate block header contents
 366     if ( !BgzfStream::CheckBlockHeader(header) )
 367         throw BamException("BgzfStream::ReadBlock", "invalid block header contents");
 368
 369     // copy header contents to compressed buffer
 370     const size_t blockLength = BamTools::UnpackUnsignedShort(&header[16]) + 1;
 371     memcpy(m_compressedBlock.Buffer, header, Constants::BGZF_BLOCK_HEADER_LENGTH);
 372
 373     // read remainder of block
 374     const size_t remaining = blockLength - Constants::BGZF_BLOCK_HEADER_LENGTH;
 375     numBytesRead = m_device->Read(&m_compressedBlock.Buffer[Constants::BGZF_BLOCK_HEADER_LENGTH], remaining);
 376
 377     // check for device error
 378     if ( numBytesRead < 0 ) {
 379         const string message = string("device error: ") + m_device->GetErrorString();
 380         throw BamException("BgzfStream::ReadBlock", message);
 381     }
 382
 383     // check that we read in expected numBytes
 384     if ( numBytesRead != static_cast<int64_t>(remaining) )
 385         throw BamException("BgzfStream::ReadBlock", "could not read data from block");
 386
 387     // decompress block data
 388     const size_t newBlockLength = InflateBlock(blockLength);
 389
 390     // update block data
 391     if ( m_blockLength != 0 )
 392         m_blockOffset = 0;
 393     m_blockAddress = blockAddress;
 394     m_blockLength  = newBlockLength;
 395 }
 396
 397 // seek to position in BGZF file
 398 void BgzfStream::Seek(const int64_t& position) {
 399
 400     BT_ASSERT_X( m_device, "BgzfStream::Seek() - trying to seek on null IO device");
 401
 402     // skip if device is not open
 403     if ( !IsOpen() ) return;
 404
 405     // determine adjusted offset & address
 406     int     blockOffset  = (position & 0xFFFF);
 407     int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL;
 408
 409     // attempt seek in file
 410     if ( m_device->IsRandomAccess() && m_device->Seek(blockAddress) ) {
 411
 412         // update block data & return success
 413         m_blockLength  = 0;
 414         m_blockAddress = blockAddress;
 415         m_blockOffset  = blockOffset;
 416     }
 417     else {
 418         stringstream s("");
 419         s << "unable to seek to position: " << position;
 420         throw BamException("BgzfStream::Seek", s.str());
 421     }
 422 }
 423
 424 void BgzfStream::SetWriteCompressed(bool ok) {
 425     m_isWriteCompressed = ok;
 426 }
 427
 428 // get file position in BGZF file
 429 int64_t BgzfStream::Tell(void) const {
 430     if ( !IsOpen() )
 431         return 0;
 432     return ( (m_blockAddress << 16) | (m_blockOffset & 0xFFFF) );
 433 }
 434
 435 // writes the supplied data into the BGZF buffer
 436 size_t BgzfStream::Write(const char* data, const size_t dataLength) {
 437
 438     BT_ASSERT_X( m_device, "BgzfStream::Write() - trying to write to null IO device");
 439     BT_ASSERT_X( (m_device->Mode() == IBamIODevice::WriteOnly),
 440                  "BgzfStream::Write() - trying to write to non-writable IO device");
 441
 442     // skip if file not open for writing
 443     if ( !IsOpen() )
 444         return 0;
 445
 446     // write blocks as needed til all data is written
 447     size_t numBytesWritten = 0;
 448     const char* input = data;
 449     const size_t blockLength = Constants::BGZF_DEFAULT_BLOCK_SIZE;
 450     while ( numBytesWritten < dataLength ) {
 451
 452         // copy data contents to uncompressed output buffer
 453         unsigned int copyLength = min(blockLength - m_blockOffset, dataLength - numBytesWritten);
 454         char* buffer = m_uncompressedBlock.Buffer;
 455         memcpy(buffer + m_blockOffset, input, copyLength);
 456
 457         // update counter
 458         m_blockOffset   += copyLength;
 459         input           += copyLength;
 460         numBytesWritten += copyLength;
 461
 462         // flush (& compress) output buffer when full
 463         if ( m_blockOffset == static_cast<int32_t>(blockLength) )
 464             FlushBlock();
 465     }
 466
 467     // return actual number of bytes written
 468     return numBytesWritten;
 469 }