// BgzfStream_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 2 September 2011(DB)
+// Last modified: 9 September 2011(DB)
// ---------------------------------------------------------------------------
// Based on BGZF routines developed at the Broad Institute.
// Provides the basic functionality for reading & writing BGZF files
// Replaces the old BGZF.* files to avoid clashing with other toolkits
// ***************************************************************************
+#include <api/internal/BamDeviceFactory_p.h>
#include <api/internal/BgzfStream_p.h>
using namespace BamTools;
using namespace BamTools::Internal;
#include <cstring>
#include <algorithm>
+#include <iostream>
using namespace std;
// constructor
BgzfStream::BgzfStream(void)
- : UncompressedBlockSize(Constants::BGZF_DEFAULT_BLOCK_SIZE)
- , CompressedBlockSize(Constants::BGZF_MAX_BLOCK_SIZE)
- , BlockLength(0)
- , BlockOffset(0)
- , BlockAddress(0)
- , IsOpen(false)
- , IsWriteOnly(false)
- , IsWriteCompressed(true)
- , Stream(NULL)
- , UncompressedBlock(NULL)
- , CompressedBlock(NULL)
+ : m_uncompressedBlockSize(Constants::BGZF_DEFAULT_BLOCK_SIZE)
+ , m_compressedBlockSize(Constants::BGZF_MAX_BLOCK_SIZE)
+ , m_blockLength(0)
+ , m_blockOffset(0)
+ , m_blockAddress(0)
+ , m_uncompressedBlock(NULL)
+ , m_compressedBlock(NULL)
+ , m_isOpen(false)
+ , m_isWriteOnly(false)
+ , m_isWriteCompressed(true)
+ , m_device(0)
+ , m_stream(NULL)
{
try {
- CompressedBlock = new char[CompressedBlockSize];
- UncompressedBlock = new char[UncompressedBlockSize];
+ m_compressedBlock = new char[m_compressedBlockSize];
+ m_uncompressedBlock = new char[m_uncompressedBlockSize];
} catch( std::bad_alloc& ba ) {
fprintf(stderr, "BgzfStream ERROR: unable to allocate memory\n");
exit(1);
// destructor
BgzfStream::~BgzfStream(void) {
- if( CompressedBlock ) delete[] CompressedBlock;
- if( UncompressedBlock ) delete[] UncompressedBlock;
+ if( m_compressedBlock ) delete[] m_compressedBlock;
+ if( m_uncompressedBlock ) delete[] m_uncompressedBlock;
}
// closes BGZF file
void BgzfStream::Close(void) {
- // skip if file not open
- if ( !IsOpen ) return;
+ // skip if no device open
+ if ( m_device == 0 )
+ return;
// if writing to file, flush the current BGZF block,
// then write an empty block (as EOF marker)
- if ( IsWriteOnly ) {
+ if ( m_device->IsOpen() && (m_device->Mode() == IBamIODevice::WriteOnly) ) {
FlushBlock();
int blockLength = DeflateBlock();
- fwrite(CompressedBlock, 1, blockLength, Stream);
+ m_device->Write(m_compressedBlock, blockLength);
}
- // flush and close stream
- fflush(Stream);
- fclose(Stream);
+ // close device
+ m_device->Close();
- // reset flags
- IsWriteCompressed = true;
- IsOpen = false;
+ // clean up & reset flags
+ delete m_device;
+ m_device = 0;
+ m_isWriteCompressed = true;
+ m_isOpen = false;
}
// compresses the current block
-int BgzfStream::DeflateBlock(void) {
+unsigned int BgzfStream::DeflateBlock(void) {
// initialize the gzip header
- char* buffer = CompressedBlock;
+ char* buffer = m_compressedBlock;
memset(buffer, 0, 18);
buffer[0] = Constants::GZIP_ID1;
buffer[1] = (char)Constants::GZIP_ID2;
buffer[14] = Constants::BGZF_LEN;
// set compression level
- const int compressionLevel = ( IsWriteCompressed ? Z_DEFAULT_COMPRESSION : 0 );
+ const int compressionLevel = ( m_isWriteCompressed ? Z_DEFAULT_COMPRESSION : 0 );
// loop to retry for blocks that do not compress enough
- int inputLength = BlockOffset;
- int compressedLength = 0;
- unsigned int bufferSize = CompressedBlockSize;
+ int inputLength = m_blockOffset;
+ unsigned int compressedLength = 0;
+ unsigned int bufferSize = m_compressedBlockSize;
while ( true ) {
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
- zs.next_in = (Bytef*)UncompressedBlock;
+ zs.next_in = (Bytef*)m_uncompressedBlock;
zs.avail_in = inputLength;
zs.next_out = (Bytef*)&buffer[Constants::BGZF_BLOCK_HEADER_LENGTH];
zs.avail_out = bufferSize - Constants::BGZF_BLOCK_HEADER_LENGTH - Constants::BGZF_BLOCK_FOOTER_LENGTH;
// store the CRC32 checksum
unsigned int crc = crc32(0, NULL, 0);
- crc = crc32(crc, (Bytef*)UncompressedBlock, inputLength);
+ crc = crc32(crc, (Bytef*)m_uncompressedBlock, inputLength);
BamTools::PackUnsignedInt(&buffer[compressedLength - 8], crc);
BamTools::PackUnsignedInt(&buffer[compressedLength - 4], inputLength);
// ensure that we have less than a block of data left
- int remaining = BlockOffset - inputLength;
+ int remaining = m_blockOffset - inputLength;
if ( remaining > 0 ) {
if ( remaining > inputLength ) {
fprintf(stderr, "BgzfStream ERROR: after deflate, remainder too large\n");
exit(1);
}
- memcpy(UncompressedBlock, UncompressedBlock + inputLength, remaining);
+ memcpy(m_uncompressedBlock, m_uncompressedBlock + inputLength, remaining);
}
// update block data
- BlockOffset = remaining;
+ m_blockOffset = remaining;
// return result
return compressedLength;
// flushes the data in the BGZF block
void BgzfStream::FlushBlock(void) {
+ BT_ASSERT_X( m_device, "BgzfStream::FlushBlock() - attempting to flush to null device" );
+
// flush all of the remaining blocks
- while ( BlockOffset > 0 ) {
+ while ( m_blockOffset > 0 ) {
// compress the data block
- int blockLength = DeflateBlock();
+ unsigned int blockLength = DeflateBlock();
// flush the data to our output stream
- int numBytesWritten = fwrite(CompressedBlock, 1, blockLength, Stream);
+ unsigned int numBytesWritten = m_device->Write(m_compressedBlock, blockLength);
if ( numBytesWritten != blockLength ) {
fprintf(stderr, "BgzfStream ERROR: expected to write %u bytes during flushing, but wrote %u bytes\n",
blockLength, numBytesWritten);
}
// update block data
- BlockAddress += blockLength;
+ m_blockAddress += blockLength;
}
}
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
- zs.next_in = (Bytef*)CompressedBlock + 18;
+ zs.next_in = (Bytef*)m_compressedBlock + 18;
zs.avail_in = blockLength - 16;
- zs.next_out = (Bytef*)UncompressedBlock;
- zs.avail_out = UncompressedBlockSize;
+ zs.next_out = (Bytef*)m_uncompressedBlock;
+ zs.avail_out = m_uncompressedBlockSize;
int status = inflateInit2(&zs, Constants::GZIP_WINDOW_BITS);
if ( status != Z_OK ) {
return zs.total_out;
}
+bool BgzfStream::IsOpen(void) const {
+ if ( m_device == 0 )
+ return false;
+ return m_device->IsOpen();
+}
+
+bool BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode) {
+
+ // close current device if necessary
+ Close();
+
+ // sanity check
+ BT_ASSERT_X( (m_device == 0), "BgzfStream::Open() - unable to properly close previous IO device" );
+
+ // retrieve new IO device depending on filename
+ m_device = BamDeviceFactory::CreateDevice(filename);
+
+ // sanity check
+ BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from filename" );
+
+ // if device fails to open
+ if ( !m_device->Open(mode) ) {
+ cerr << "BgzfStream::Open() - unable to open IO device:" << endl;
+ cerr << m_device->ErrorString();
+ return false;
+ }
+
+ // otherwise, set flag & return true
+ m_isOpen = true;
+ m_isWriteOnly = ( mode == IBamIODevice::WriteOnly );
+ return true;
+
+}
+
// opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing)
bool BgzfStream::Open(const string& filename, const char* mode) {
// close current stream, if necessary, before opening next
- if ( IsOpen ) Close();
+ if ( m_isOpen ) Close();
// determine open mode
if ( strcmp(mode, "rb") == 0 )
- IsWriteOnly = false;
+ m_isWriteOnly = false;
else if ( strcmp(mode, "wb") == 0)
- IsWriteOnly = true;
+ m_isWriteOnly = true;
else {
fprintf(stderr, "BgzfStream ERROR: unknown file mode: %s\n", mode);
return false;
// open BGZF stream on a file
if ( (filename != "stdin") && (filename != "stdout") && (filename != "-"))
- Stream = fopen(filename.c_str(), mode);
+ m_stream = fopen(filename.c_str(), mode);
// open BGZF stream on stdin
else if ( (filename == "stdin" || filename == "-") && (strcmp(mode, "rb") == 0 ) )
- Stream = freopen(NULL, mode, stdin);
+ m_stream = freopen(NULL, mode, stdin);
// open BGZF stream on stdout
else if ( (filename == "stdout" || filename == "-") && (strcmp(mode, "wb") == 0) )
- Stream = freopen(NULL, mode, stdout);
+ m_stream = freopen(NULL, mode, stdout);
- if ( !Stream ) {
+ if ( !m_stream ) {
fprintf(stderr, "BgzfStream ERROR: unable to open file %s\n", filename.c_str() );
return false;
}
// set flag & return success
- IsOpen = true;
+ m_isOpen = true;
return true;
}
// reads BGZF data into a byte buffer
-int BgzfStream::Read(char* data, const unsigned int dataLength) {
+unsigned int BgzfStream::Read(char* data, const unsigned int dataLength) {
- // if stream not open for reading (or empty request)
- if ( !IsOpen || IsWriteOnly || dataLength == 0 )
+ if ( dataLength == 0 )
+ return 0;
+
+ // if stream not open for reading
+ BT_ASSERT_X( m_device, "BgzfStream::Read() - trying to read from null device");
+ if ( !m_device->IsOpen() || (m_device->Mode() != IBamIODevice::ReadOnly) )
return 0;
// read blocks as needed until desired data length is retrieved
while ( numBytesRead < dataLength ) {
// determine bytes available in current block
- int bytesAvailable = BlockLength - BlockOffset;
+ int bytesAvailable = m_blockLength - m_blockOffset;
// read (and decompress) next block if needed
if ( bytesAvailable <= 0 ) {
if ( !ReadBlock() ) return -1;
- bytesAvailable = BlockLength - BlockOffset;
+ bytesAvailable = m_blockLength - m_blockOffset;
if ( bytesAvailable <= 0 ) break;
}
// copy data from uncompressed source buffer into data destination buffer
- char* buffer = UncompressedBlock;
+ char* buffer = m_uncompressedBlock;
int copyLength = min( (int)(dataLength-numBytesRead), bytesAvailable );
- memcpy(output, buffer + BlockOffset, copyLength);
+ memcpy(output, buffer + m_blockOffset, copyLength);
// update counters
- BlockOffset += copyLength;
- output += copyLength;
- numBytesRead += copyLength;
+ m_blockOffset += copyLength;
+ output += copyLength;
+ numBytesRead += copyLength;
}
// update block data
- if ( BlockOffset == BlockLength ) {
- BlockAddress = ftell64(Stream);
- BlockOffset = 0;
- BlockLength = 0;
+ if ( m_blockOffset == m_blockLength ) {
+ m_blockAddress = m_device->Tell();
+ m_blockOffset = 0;
+ m_blockLength = 0;
}
return numBytesRead;
// reads a BGZF block
bool BgzfStream::ReadBlock(void) {
- char header[Constants::BGZF_BLOCK_HEADER_LENGTH];
- int64_t blockAddress = ftell64(Stream);
+ BT_ASSERT_X( m_device, "BgzfStream::ReadBlock() - trying to read from null IO device");
+
+ // store block's starting address
+ int64_t blockAddress = m_device->Tell();
// read block header from file
- int count = fread(header, 1, sizeof(header), Stream);
+ char header[Constants::BGZF_BLOCK_HEADER_LENGTH];
+ int numBytesRead = m_device->Read(header, Constants::BGZF_BLOCK_HEADER_LENGTH);
// if block header empty
- if ( count == 0 ) {
- BlockLength = 0;
+ if ( numBytesRead == 0 ) {
+ m_blockLength = 0;
return true;
}
// if block header invalid size
- if ( count != sizeof(header) ) {
+ if ( numBytesRead != Constants::BGZF_BLOCK_HEADER_LENGTH ) {
fprintf(stderr, "BgzfStream ERROR: read block failed - could not read block header\n");
return false;
}
// copy header contents to compressed buffer
int blockLength = BamTools::UnpackUnsignedShort(&header[16]) + 1;
- char* compressedBlock = CompressedBlock;
+ char* compressedBlock = m_compressedBlock;
memcpy(compressedBlock, header, Constants::BGZF_BLOCK_HEADER_LENGTH);
int remaining = blockLength - Constants::BGZF_BLOCK_HEADER_LENGTH;
// read remainder of block
- count = fread(&compressedBlock[Constants::BGZF_BLOCK_HEADER_LENGTH], 1, remaining, Stream);
- if ( count != remaining ) {
+ numBytesRead = m_device->Read(&compressedBlock[Constants::BGZF_BLOCK_HEADER_LENGTH], remaining);
+ if ( numBytesRead != remaining ) {
fprintf(stderr, "BgzfStream ERROR: read block failed - could not read data from block\n");
return false;
}
// decompress block data
- count = InflateBlock(blockLength);
- if ( count < 0 ) {
+ numBytesRead = InflateBlock(blockLength);
+ if ( numBytesRead < 0 ) {
fprintf(stderr, "BgzfStream ERROR: read block failed - could not decompress block data\n");
return false;
}
// update block data
- if ( BlockLength != 0 )
- BlockOffset = 0;
- BlockAddress = blockAddress;
- BlockLength = count;
+ if ( m_blockLength != 0 )
+ m_blockOffset = 0;
+ m_blockAddress = blockAddress;
+ m_blockLength = numBytesRead;
// return success
return true;
// seek to position in BGZF file
bool BgzfStream::Seek(const int64_t& position) {
- // skip if not open
- if ( !IsOpen ) return false;
+ BT_ASSERT_X( m_device, "BgzfStream::Seek() - trying to seek on null IO device");
+
+ // skip if not open or not seek-able
+ if ( !IsOpen() /*|| !m_device->IsRandomAccess()*/ ) {
+ cerr << "BgzfStream::Seek() - device not open" << endl;
+ return false;
+ }
// determine adjusted offset & address
int blockOffset = (position & 0xFFFF);
int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL;
// attempt seek in file
- if ( fseek64(Stream, blockAddress, SEEK_SET) != 0 ) {
- fprintf(stderr, "BgzfStream ERROR: unable to seek in file\n");
+ if ( !m_device->Seek(blockAddress) ) {
+ cerr << "BgzfStream ERROR: unable to seek in file" << endl;
return false;
}
// update block data & return success
- BlockLength = 0;
- BlockAddress = blockAddress;
- BlockOffset = blockOffset;
+ m_blockLength = 0;
+ m_blockAddress = blockAddress;
+ m_blockOffset = blockOffset;
return true;
}
void BgzfStream::SetWriteCompressed(bool ok) {
- IsWriteCompressed = ok;
+ m_isWriteCompressed = ok;
}
// get file position in BGZF file
int64_t BgzfStream::Tell(void) const {
- if ( !IsOpen )
- return 0;
- return ( (BlockAddress << 16) | (BlockOffset & 0xFFFF) );
+ if ( !m_isOpen ) return 0;
+ return ( (m_blockAddress << 16) | (m_blockOffset & 0xFFFF) );
}
// writes the supplied data into the BGZF buffer
-unsigned int BgzfStream::Write(const char* data, const unsigned int dataLen) {
+unsigned int BgzfStream::Write(const char* data, const unsigned int dataLength) {
- // skip if file not open for writing
- if ( !IsOpen || !IsWriteOnly ) return false;
+ BT_ASSERT_X( m_device, "BgzfStream::Write() - trying to write to null IO device");
+ BT_ASSERT_X( (m_device->Mode() == IBamIODevice::WriteOnly),
+ "BgzfStream::Write() - trying to write to non-writable IO device");
// write blocks as needed til all data is written
unsigned int numBytesWritten = 0;
const char* input = data;
- unsigned int blockLength = UncompressedBlockSize;
- while ( numBytesWritten < dataLen ) {
+ unsigned int blockLength = m_uncompressedBlockSize;
+ while ( numBytesWritten < dataLength ) {
// copy data contents to uncompressed output buffer
- unsigned int copyLength = min(blockLength - BlockOffset, dataLen - numBytesWritten);
- char* buffer = UncompressedBlock;
- memcpy(buffer + BlockOffset, input, copyLength);
+ unsigned int copyLength = min(blockLength - m_blockOffset, dataLength - numBytesWritten);
+ char* buffer = m_uncompressedBlock;
+ memcpy(buffer + m_blockOffset, input, copyLength);
// update counter
- BlockOffset += copyLength;
+ m_blockOffset += copyLength;
input += copyLength;
numBytesWritten += copyLength;
// flush (& compress) output buffer when full
- if ( BlockOffset == blockLength ) FlushBlock();
+ if ( m_blockOffset == blockLength )
+ FlushBlock();
}
// return result
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