// BgzfStream_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 October 2011(DB)
+// Last modified: 11 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>
+#include "api/BamAux.h"
+#include "api/BamConstants.h"
+#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 "zlib.h"
+
#include <cstring>
#include <algorithm>
#include <iostream>
// RaiiWrapper implementation
// ----------------------------
-BgzfStream::RaiiWrapper::RaiiWrapper(void)
- : Stream(0)
-{
+BgzfStream::RaiiWrapper::RaiiWrapper(void) {
CompressedBlock = new char[Constants::BGZF_MAX_BLOCK_SIZE];
UncompressedBlock = new char[Constants::BGZF_DEFAULT_BLOCK_SIZE];
}
delete[] UncompressedBlock;
CompressedBlock = 0;
UncompressedBlock = 0;
-
- if ( Stream ) {
- fflush(Stream);
- fclose(Stream);
- Stream = 0;
- }
}
// ---------------------------
: m_blockLength(0)
, m_blockOffset(0)
, m_blockAddress(0)
- , m_isOpen(false)
- , m_isWriteOnly(false)
, m_isWriteCompressed(true)
, m_device(0)
{ }
void BgzfStream::Close(void) {
// skip if no device open
- if ( m_device == 0 )
- return;
+ if ( m_device == 0 ) return;
// if writing to file, flush the current BGZF block,
// then write an empty block (as EOF marker)
delete m_device;
m_device = 0;
- // ??
- fflush(Resources.Stream);
- fclose(Resources.Stream);
- Resources.Stream = 0;
-
// reset state
m_blockLength = 0;
m_blockOffset = 0;
m_blockAddress = 0;
- m_isOpen = false;
- m_isWriteOnly = false;
m_isWriteCompressed = true;
-
}
// compresses the current block
const int compressionLevel = ( m_isWriteCompressed ? Z_DEFAULT_COMPRESSION : 0 );
// loop to retry for blocks that do not compress enough
- int inputLength = BlockOffset;
+ int inputLength = m_blockOffset;
size_t compressedLength = 0;
const unsigned int bufferSize = Constants::BGZF_MAX_BLOCK_SIZE;
deflateEnd(&zs);
- // if error status
- if ( status != Z_OK )
- throw BamException("BgzfStream::DeflateBlock", "zlib deflate failed");
-
- // not enough space available in buffer
+ // there was 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;
+ if ( status == Z_OK ) {
+ inputLength -= 1024;
+ if ( inputLength < 0 )
+ throw BamException("BgzfStream::DeflateBlock", "input reduction failed");
+ continue;
+ }
+
+ throw BamException("BgzfStream::DeflateBlock", "zlib deflate failed");
}
// finalize the compression routine
return m_device->IsOpen();
}
-bool BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode) {
+void 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)
-void BgzfStream::Open(const string& filename, const char* mode) {
-
- // make sure we're starting with fresh state
- if ( IsOpen() )
- Close();
-
- // determine open mode
- if ( strcmp(mode, "rb") == 0 )
- m_isWriteOnly = false;
- else if ( strcmp(mode, "wb") == 0)
- m_isWriteOnly = true;
- else {
- const string message = string("unknown file mode: ") + mode;
+ const string deviceError = m_device->GetErrorString();
+ const string message = string("could not open BGZF stream: \n\t") + deviceError;
throw BamException("BgzfStream::Open", message);
}
-
- // open BGZF stream on a file
- if ( (filename != "stdin") && (filename != "stdout") && (filename != "-"))
- Resources.Stream = fopen(filename.c_str(), mode);
-
- // open BGZF stream on stdin
- else if ( (filename == "stdin" || filename == "-") && (strcmp(mode, "rb") == 0 ) )
- Resources.Stream = freopen(NULL, mode, stdin);
-
- // open BGZF stream on stdout
- else if ( (filename == "stdout" || filename == "-") && (strcmp(mode, "wb") == 0) )
- Resources.Stream = freopen(NULL, mode, stdout);
-
- // ensure valid Stream
- if ( !Resources.Stream ) {
- const string message = string("unable to open file: ") + filename;
- throw BamException("BgzfStream::Open", message);
- }
-
- // set flag & return success
- m_isOpen = true;
- return true;
}
// reads BGZF data into a byte buffer
return 0;
// read blocks as needed until desired data length is retrieved
+ char* output = data;
size_t numBytesRead = 0;
while ( numBytesRead < dataLength ) {
// copy data from uncompressed source buffer into data destination buffer
const size_t copyLength = min( (dataLength-numBytesRead), (size_t)bytesAvailable );
- memcpy(data, Resources.UncompressedBlock + m_blockOffset, copyLength);
+ memcpy(output, Resources.UncompressedBlock + m_blockOffset, copyLength);
// update counters
- m_blockOffset += copyLength;
- data += copyLength;
- numBytesRead += copyLength;
+ m_blockOffset += copyLength;
+ output += copyLength;
+ numBytesRead += copyLength;
}
// update block data
if ( m_blockOffset == m_blockLength ) {
m_blockAddress = m_device->Tell();
- m_BlockOffset = 0;
- m_BlockLength = 0;
+ m_blockOffset = 0;
+ m_blockLength = 0;
}
// if block header empty
if ( numBytesRead == 0 ) {
m_blockLength = 0;
- return true;
+ return;
}
// if block header invalid size
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;
- }
+ // 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 ( !m_device->Seek(blockAddress) ) {
+ if ( m_device->IsRandomAccess() && m_device->Seek(blockAddress) ) {
+
+ // 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());
}
-
- // update block data & return success
- m_blockLength = 0;
- m_blockAddress = blockAddress;
- m_blockOffset = blockOffset;
}
void BgzfStream::SetWriteCompressed(bool ok) {
// get file position in BGZF file
int64_t BgzfStream::Tell(void) const {
- if ( !m_isOpen ) return 0;
+ if ( !IsOpen() )
+ return 0;
return ( (m_blockAddress << 16) | (m_blockOffset & 0xFFFF) );
}
"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
size_t numBytesWritten = 0;
projects / bamtools.git / blobdiff