// ***************************************************************************
// BgzfStream_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011(DB)
+// Last modified: 7 October 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/BamException_p.h>
#include <api/internal/BgzfStream_p.h>
using namespace BamTools;
using namespace BamTools::Internal;
#include <cstring>
#include <algorithm>
+#include <iostream>
+#include <sstream>
using namespace std;
+// ----------------------------
+// RaiiWrapper implementation
+// ----------------------------
+
+BgzfStream::RaiiWrapper::RaiiWrapper(void) {
+ CompressedBlock = new char[Constants::BGZF_MAX_BLOCK_SIZE];
+ UncompressedBlock = new char[Constants::BGZF_DEFAULT_BLOCK_SIZE];
+}
+
+BgzfStream::RaiiWrapper::~RaiiWrapper(void) {
+
+ // clean up buffers
+ delete[] CompressedBlock;
+ delete[] UncompressedBlock;
+ CompressedBlock = 0;
+ UncompressedBlock = 0;
+}
+
+// ---------------------------
+// BgzfStream implementation
+// ---------------------------
+
// 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)
-{
- try {
- CompressedBlock = new char[CompressedBlockSize];
- UncompressedBlock = new char[UncompressedBlockSize];
- } catch( std::bad_alloc& ba ) {
- fprintf(stderr, "BgzfStream ERROR: unable to allocate memory\n");
- exit(1);
- }
-}
+ : m_blockLength(0)
+ , m_blockOffset(0)
+ , m_blockAddress(0)
+ , m_isWriteCompressed(true)
+ , m_device(0)
+{ }
// destructor
BgzfStream::~BgzfStream(void) {
- if( CompressedBlock ) delete[] CompressedBlock;
- if( UncompressedBlock ) delete[] UncompressedBlock;
+ Close();
+}
+
+// checks BGZF block header
+bool BgzfStream::CheckBlockHeader(char* header) {
+ return (header[0] == Constants::GZIP_ID1 &&
+ header[1] == Constants::GZIP_ID2 &&
+ header[2] == Z_DEFLATED &&
+ (header[3] & Constants::FLG_FEXTRA) != 0 &&
+ BamTools::UnpackUnsignedShort(&header[10]) == Constants::BGZF_XLEN &&
+ header[12] == Constants::BGZF_ID1 &&
+ header[13] == Constants::BGZF_ID2 &&
+ BamTools::UnpackUnsignedShort(&header[14]) == Constants::BGZF_LEN );
}
// closes BGZF file
void BgzfStream::Close(void) {
- // skip if file not open
- if ( !IsOpen ) return;
+ // reset state
+ m_blockLength = 0;
+ m_blockOffset = 0;
+ m_blockAddress = 0;
+ m_isWriteCompressed = true;
+
+ // 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);
+ const size_t blockLength = DeflateBlock();
+ m_device->Write(Resources.CompressedBlock, blockLength);
}
- // flush and close stream
- fflush(Stream);
- fclose(Stream);
-
- // reset flags
- IsWriteCompressed = true;
- IsOpen = false;
+ // close device
+ m_device->Close();
+ delete m_device;
+ m_device = 0;
}
// compresses the current block
-int BgzfStream::DeflateBlock(void) {
+size_t BgzfStream::DeflateBlock(void) {
// initialize the gzip header
- char* buffer = CompressedBlock;
+ char* buffer = Resources.CompressedBlock;
memset(buffer, 0, 18);
buffer[0] = Constants::GZIP_ID1;
- buffer[1] = (char)Constants::GZIP_ID2;
+ buffer[1] = Constants::GZIP_ID2;
buffer[2] = Constants::CM_DEFLATE;
buffer[3] = Constants::FLG_FEXTRA;
- buffer[9] = (char)Constants::OS_UNKNOWN;
+ buffer[9] = Constants::OS_UNKNOWN;
buffer[10] = Constants::BGZF_XLEN;
buffer[12] = Constants::BGZF_ID1;
buffer[13] = Constants::BGZF_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;
+ size_t compressedLength = 0;
+ const unsigned int bufferSize = Constants::BGZF_MAX_BLOCK_SIZE;
while ( true ) {
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
- zs.next_in = (Bytef*)UncompressedBlock;
+ zs.next_in = (Bytef*)Resources.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;
+ zs.avail_out = bufferSize -
+ Constants::BGZF_BLOCK_HEADER_LENGTH -
+ Constants::BGZF_BLOCK_FOOTER_LENGTH;
// initialize the zlib compression algorithm
- if ( deflateInit2(&zs,
- compressionLevel,
- Z_DEFLATED,
- Constants::GZIP_WINDOW_BITS,
- Constants::Z_DEFAULT_MEM_LEVEL,
- Z_DEFAULT_STRATEGY) != Z_OK )
- {
- fprintf(stderr, "BgzfStream ERROR: zlib deflate initialization failed\n");
- exit(1);
- }
+ int status = deflateInit2(&zs,
+ compressionLevel,
+ Z_DEFLATED,
+ Constants::GZIP_WINDOW_BITS,
+ Constants::Z_DEFAULT_MEM_LEVEL,
+ Z_DEFAULT_STRATEGY);
+ if ( status != Z_OK )
+ throw BamException("BgzfStream::DeflateBlock", "zlib deflateInit2 failed");
// compress the data
- int status = deflate(&zs, Z_FINISH);
+ status = deflate(&zs, Z_FINISH);
+
+ // if not at stream end
if ( status != Z_STREAM_END ) {
deflateEnd(&zs);
- // reduce the input length and try again
- if ( status == Z_OK ) {
- inputLength -= 1024;
- if ( inputLength < 0 ) {
- fprintf(stderr, "BgzfStream ERROR: input reduction failed\n");
- exit(1);
- }
- continue;
- }
-
- fprintf(stderr, "BgzfStream ERROR: zlib::deflateEnd() failed\n");
- exit(1);
- }
+ // if error status
+ if ( status != Z_OK )
+ throw BamException("BgzfStream::DeflateBlock", "zlib deflate failed");
- // finalize the compression routine
- if ( deflateEnd(&zs) != Z_OK ) {
- fprintf(stderr, "BgzfStream ERROR: zlib::deflateEnd() failed\n");
- exit(1);
- }
-
- compressedLength = zs.total_out;
- compressedLength += Constants::BGZF_BLOCK_HEADER_LENGTH + Constants::BGZF_BLOCK_FOOTER_LENGTH;
- if ( compressedLength > Constants::BGZF_MAX_BLOCK_SIZE ) {
- fprintf(stderr, "BgzfStream ERROR: deflate overflow\n");
- exit(1);
+ // not enough space available in buffer
+ // try to reduce the input length & re-start loop
+ inputLength -= 1024;
+ if ( inputLength <= 0 )
+ throw BamException("BgzfStream::DeflateBlock", "input reduction failed");
+ continue;
}
+ // finalize the compression routine
+ status = deflateEnd(&zs);
+ if ( status != Z_OK )
+ throw BamException("BgzfStream::DeflateBlock", "zlib deflateEnd failed");
+
+ // update compressedLength
+ compressedLength = zs.total_out +
+ Constants::BGZF_BLOCK_HEADER_LENGTH +
+ Constants::BGZF_BLOCK_FOOTER_LENGTH;
+ if ( compressedLength > Constants::BGZF_MAX_BLOCK_SIZE )
+ throw BamException("BgzfStream::DeflateBlock", "deflate overflow");
+
+ // quit while loop
break;
}
// store the compressed length
- BamTools::PackUnsignedShort(&buffer[16], (unsigned short)(compressedLength - 1));
+ BamTools::PackUnsignedShort(&buffer[16], static_cast<uint16_t>(compressedLength - 1));
// store the CRC32 checksum
- unsigned int crc = crc32(0, NULL, 0);
- crc = crc32(crc, (Bytef*)UncompressedBlock, inputLength);
+ uint32_t crc = crc32(0, NULL, 0);
+ crc = crc32(crc, (Bytef*)Resources.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);
+ if ( remaining > inputLength )
+ throw BamException("BgzfStream::DeflateBlock", "after deflate, remainder too large");
+ memcpy(Resources.UncompressedBlock, Resources.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();
+ const size_t blockLength = DeflateBlock();
- // flush the data to our output stream
- int numBytesWritten = fwrite(CompressedBlock, 1, blockLength, Stream);
+ // flush the data to our output device
+ const size_t numBytesWritten = m_device->Write(Resources.CompressedBlock, blockLength);
if ( numBytesWritten != blockLength ) {
- fprintf(stderr, "BgzfStream ERROR: expected to write %u bytes during flushing, but wrote %u bytes\n",
- blockLength, numBytesWritten);
- exit(1);
+ stringstream s("");
+ s << "expected to write " << blockLength
+ << " bytes during flushing, but wrote " << numBytesWritten;
+ throw BamException("BgzfStream::FlushBlock", s.str());
}
// update block data
- BlockAddress += blockLength;
+ m_blockAddress += blockLength;
}
}
// decompresses the current block
-int BgzfStream::InflateBlock(const int& blockLength) {
+size_t BgzfStream::InflateBlock(const size_t& blockLength) {
- // inflate the data from compressed buffer into uncompressed buffer
+ // setup zlib stream object
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
- zs.next_in = (Bytef*)CompressedBlock + 18;
+ zs.next_in = (Bytef*)Resources.CompressedBlock + 18;
zs.avail_in = blockLength - 16;
- zs.next_out = (Bytef*)UncompressedBlock;
- zs.avail_out = UncompressedBlockSize;
+ zs.next_out = (Bytef*)Resources.UncompressedBlock;
+ zs.avail_out = Constants::BGZF_DEFAULT_BLOCK_SIZE;
+ // initialize
int status = inflateInit2(&zs, Constants::GZIP_WINDOW_BITS);
- if ( status != Z_OK ) {
- fprintf(stderr, "BgzfStream ERROR: could not decompress block - zlib::inflateInit() failed\n");
- return -1;
- }
+ if ( status != Z_OK )
+ throw BamException("BgzfStream::InflateBlock", "zlib inflateInit failed");
+ // decompress
status = inflate(&zs, Z_FINISH);
if ( status != Z_STREAM_END ) {
inflateEnd(&zs);
- fprintf(stderr, "BgzfStream ERROR: could not decompress block - zlib::inflate() failed\n");
- return -1;
+ throw BamException("BgzfStream::InflateBlock", "zlib inflate failed");
}
+ // finalize
status = inflateEnd(&zs);
if ( status != Z_OK ) {
- fprintf(stderr, "BgzfStream ERROR: could not decompress block - zlib::inflateEnd() failed\n");
- return -1;
+ inflateEnd(&zs);
+ throw BamException("BgzfStream::InflateBlock", "zlib inflateEnd failed");
}
// return result
return zs.total_out;
}
-// 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();
-
- // determine open mode
- if ( strcmp(mode, "rb") == 0 )
- IsWriteOnly = false;
- else if ( strcmp(mode, "wb") == 0)
- IsWriteOnly = true;
- else {
- fprintf(stderr, "BgzfStream ERROR: unknown file mode: %s\n", mode);
+bool BgzfStream::IsOpen(void) const {
+ if ( m_device == 0 )
return false;
- }
+ return m_device->IsOpen();
+}
- // open BGZF stream on a file
- if ( (filename != "stdin") && (filename != "stdout") )
- Stream = fopen(filename.c_str(), mode);
+void BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode) {
- // open BGZF stream on stdin
- else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) )
- Stream = freopen(NULL, mode, stdin);
+ // close current device if necessary
+ Close();
+ BT_ASSERT_X( (m_device == 0), "BgzfStream::Open() - unable to properly close previous IO device" );
- // open BGZF stream on stdout
- else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) )
- Stream = freopen(NULL, mode, stdout);
+ // retrieve new IO device depending on filename
+ m_device = BamDeviceFactory::CreateDevice(filename);
+ BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from filename" );
- if ( !Stream ) {
- fprintf(stderr, "BgzfStream ERROR: unable to open file %s\n", filename.c_str() );
- return false;
+ // if device fails to open
+ if ( !m_device->Open(mode) ) {
+ const string deviceError = m_device->GetErrorString();
+ const string message = string("could not open BGZF stream: \n\t") + deviceError;
+ throw BamException("BgzfStream::Open", message);
}
-
- // set flag & return success
- IsOpen = true;
- return true;
}
// reads BGZF data into a byte buffer
-int BgzfStream::Read(char* data, const unsigned int dataLength) {
+size_t BgzfStream::Read(char* data, const size_t dataLength) {
+
+ if ( dataLength == 0 )
+ return 0;
- // if stream not open for reading (or empty request)
- if ( !IsOpen || IsWriteOnly || dataLength == 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
- char* output = data;
- unsigned int numBytesRead = 0;
+ size_t numBytesRead = 0;
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;
- if ( bytesAvailable <= 0 ) break;
+ ReadBlock();
+ bytesAvailable = m_blockLength - m_blockOffset;
+ if ( bytesAvailable <= 0 )
+ break;
}
// copy data from uncompressed source buffer into data destination buffer
- char* buffer = UncompressedBlock;
- int copyLength = min( (int)(dataLength-numBytesRead), bytesAvailable );
- memcpy(output, buffer + BlockOffset, copyLength);
+ const size_t copyLength = min( (dataLength-numBytesRead), (size_t)bytesAvailable );
+ memcpy(data, Resources.UncompressedBlock + m_blockOffset, copyLength);
// update counters
- BlockOffset += copyLength;
- output += copyLength;
+ m_blockOffset += copyLength;
+ data += 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 actual number of bytes read
return numBytesRead;
}
// reads a BGZF block
-bool BgzfStream::ReadBlock(void) {
+void 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];
+ size_t numBytesRead = m_device->Read(header, Constants::BGZF_BLOCK_HEADER_LENGTH);
// if block header empty
- if ( count == 0 ) {
- BlockLength = 0;
- return true;
+ if ( numBytesRead == 0 ) {
+ m_blockLength = 0;
+ return;
}
// if block header invalid size
- if ( count != sizeof(header) ) {
- fprintf(stderr, "BgzfStream ERROR: read block failed - could not read block header\n");
- return false;
- }
+ if ( numBytesRead != Constants::BGZF_BLOCK_HEADER_LENGTH )
+ throw BamException("BgzfStream::ReadBlock", "invalid block header size");
// validate block header contents
- if ( !BgzfStream::CheckBlockHeader(header) ) {
- fprintf(stderr, "BgzfStream ERROR: read block failed - invalid block header\n");
- return false;
- }
+ if ( !BgzfStream::CheckBlockHeader(header) )
+ throw BamException("BgzfStream::ReadBlock", "invalid block header contents");
// copy header contents to compressed buffer
- int blockLength = BamTools::UnpackUnsignedShort(&header[16]) + 1;
- char* compressedBlock = CompressedBlock;
- memcpy(compressedBlock, header, Constants::BGZF_BLOCK_HEADER_LENGTH);
- int remaining = blockLength - Constants::BGZF_BLOCK_HEADER_LENGTH;
+ const size_t blockLength = BamTools::UnpackUnsignedShort(&header[16]) + 1;
+ memcpy(Resources.CompressedBlock, header, Constants::BGZF_BLOCK_HEADER_LENGTH);
// read remainder of block
- count = fread(&compressedBlock[Constants::BGZF_BLOCK_HEADER_LENGTH], 1, remaining, Stream);
- if ( count != remaining ) {
- fprintf(stderr, "BgzfStream ERROR: read block failed - could not read data from block\n");
- return false;
- }
+ const size_t remaining = blockLength - Constants::BGZF_BLOCK_HEADER_LENGTH;
+ numBytesRead = m_device->Read(&Resources.CompressedBlock[Constants::BGZF_BLOCK_HEADER_LENGTH], remaining);
+ if ( numBytesRead != remaining )
+ throw BamException("BgzfStream::ReadBlock", "could not read data from block");
// decompress block data
- count = InflateBlock(blockLength);
- if ( count < 0 ) {
- fprintf(stderr, "BgzfStream ERROR: read block failed - could not decompress block data\n");
- return false;
- }
+ numBytesRead = InflateBlock(blockLength);
// update block data
- if ( BlockLength != 0 )
- BlockOffset = 0;
- BlockAddress = blockAddress;
- BlockLength = count;
-
- // return success
- return true;
+ if ( m_blockLength != 0 )
+ m_blockOffset = 0;
+ m_blockAddress = blockAddress;
+ m_blockLength = numBytesRead;
}
// seek to position in BGZF file
-bool BgzfStream::Seek(int64_t position) {
+void BgzfStream::Seek(const int64_t& position) {
+
+ BT_ASSERT_X( m_device, "BgzfStream::Seek() - trying to seek on null IO device");
- // skip if not open
- if ( !IsOpen ) return false;
+ // skip if device is not open
+ if ( !IsOpen() ) return;
// 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");
- return false;
- }
+ if ( m_device->IsRandomAccess() && m_device->Seek(blockAddress) ) {
- // update block data
- BlockLength = 0;
- BlockAddress = blockAddress;
- BlockOffset = blockOffset;
-
- // return success
- return true;
+ // update block data & return success
+ m_blockLength = 0;
+ m_blockAddress = blockAddress;
+ m_blockOffset = blockOffset;
+ }
+ else {
+ stringstream s("");
+ s << "unable to seek to position: " << position;
+ throw BamException("BgzfStream::Seek", s.str());
+ }
}
void BgzfStream::SetWriteCompressed(bool ok) {
- IsWriteCompressed = ok;
+ m_isWriteCompressed = ok;
}
// get file position in BGZF file
-int64_t BgzfStream::Tell(void) {
-
- // skip if file not open
- if ( !IsOpen ) return false;
-
- // otherwise return file pointer position
- return ( (BlockAddress << 16) | (BlockOffset & 0xFFFF) );
+int64_t BgzfStream::Tell(void) const {
+ if ( !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) {
+size_t BgzfStream::Write(const char* data, const size_t dataLength) {
+
+ 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");
// skip if file not open for writing
- if ( !IsOpen || !IsWriteOnly ) return false;
+ if ( !IsOpen() )
+ return 0;
// write blocks as needed til all data is written
- unsigned int numBytesWritten = 0;
+ size_t numBytesWritten = 0;
const char* input = data;
- unsigned int blockLength = UncompressedBlockSize;
- while ( numBytesWritten < dataLen ) {
+ const size_t blockLength = Constants::BGZF_DEFAULT_BLOCK_SIZE;
+ 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 = Resources.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
+ // return actual number of bytes written
return numBytesWritten;
}
projects / bamtools.git / blobdiff