internal/BamToolsIndex_p.cpp
internal/BamWriter_p.cpp
internal/BgzfStream_p.cpp
+ internal/ILocalIODevice_p.cpp
+ internal/IRemoteIODevice_p.cpp
internal/SamFormatParser_p.cpp
internal/SamFormatPrinter_p.cpp
internal/SamHeaderValidator_p.cpp
// IBamIODevice interface
public:
+
+ // pure virtuals
virtual void Close(void) =0;
virtual bool IsRandomAccess(void) const =0;
virtual bool Open(const OpenMode mode) =0;
virtual bool Seek(const int64_t& position) =0;
virtual int64_t Tell(void) const =0;
virtual size_t Write(const char* data, const unsigned int numBytes) =0;
- public:
+
+ // default implementation provided
virtual std::string ErrorString(void);
virtual bool IsOpen(void) const;
virtual OpenMode Mode(void) const;
// BamFile_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 9 September 2011 (DB)
// ---------------------------------------------------------------------------
-// Provides reading of local BAM files
+// Provides BAM file-specific IO behavior
// ***************************************************************************
#include <api/internal/BamFile_p.h>
using namespace BamTools::Internal;
#include <cstdio>
+#include <iostream>
using namespace std;
BamFile::BamFile(const string& filename)
- : IBamIODevice()
- , m_stream(0)
+ : ILocalIODevice()
, m_filename(filename)
{ }
-BamFile::~BamFile(void) {
- Close();
-}
+BamFile::~BamFile(void) { }
void BamFile::Close(void) {
-
- // skip if not open
- if ( !IsOpen() )
- return;
-
- // flush & close FILE*
- fflush(m_stream);
- fclose(m_stream);
-
- // reset internals
- m_mode = IBamIODevice::NotOpen;
- m_stream = 0;
- m_filename.clear();
+ if ( IsOpen() ) {
+ m_filename.clear();
+ ILocalIODevice::Close();
+ }
}
bool BamFile::IsRandomAccess(void) const {
return true;
}
-size_t BamFile::Read(char* data, const unsigned int numBytes) {
- BT_ASSERT_X( m_stream, "BamFile::Read() - null stream" );
- BT_ASSERT_X( (m_mode == IBamIODevice::ReadOnly), "BamFile::Read() - device not in read-only mode");
- return fread(data, sizeof(char), numBytes, m_stream);
-}
-
bool BamFile::Seek(const int64_t& position) {
BT_ASSERT_X( m_stream, "BamFile::Seek() - null stream" );
+ cerr << "BamFile::Seek() - about to attempt seek" << endl;
return ( fseek64(m_stream, position, SEEK_SET) == 0);
}
-
-int64_t BamFile::Tell(void) const {
- BT_ASSERT_X( m_stream, "BamFile::Tell() - null stream" );
- return ftell64(m_stream);
-}
-
-size_t BamFile::Write(const char* data, const unsigned int numBytes) {
- BT_ASSERT_X( m_stream, "BamFile::Write() - null stream" );
- BT_ASSERT_X( (m_mode == IBamIODevice::WriteOnly), "BamFile::Write() - device not in write-only mode" );
- return fwrite(data, sizeof(char), numBytes, m_stream);
-}
// BamFile_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 9 September 2011 (DB)
// ---------------------------------------------------------------------------
-// Provides reading/writing of local BAM files
+// Provides BAM file-specific IO behavior
// ***************************************************************************
#ifndef BAMFILE_P_H
//
// We mean it.
-#include <api/IBamIODevice.h>
+#include <api/internal/ILocalIODevice_p.h>
#include <string>
namespace BamTools {
namespace Internal {
-class BamFile : public IBamIODevice {
+class BamFile : public ILocalIODevice {
// ctor & dtor
public:
BamFile(const std::string& filename);
~BamFile(void);
- // IBamIODevice implementation
+ // ILocalIODevice implementation
public:
void Close(void);
bool IsRandomAccess(void) const;
bool Open(const IBamIODevice::OpenMode mode);
- size_t Read(char* data, const unsigned int numBytes);
bool Seek(const int64_t& position);
- int64_t Tell(void) const;
- size_t Write(const char* data, const unsigned int numBytes);
-
- // internal methods
- private:
// data members
private:
- FILE* m_stream;
std::string m_filename;
};
// BamPipe_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 9 September 2011 (DB)
// ---------------------------------------------------------------------------
-// Provides reading/writing of piped BAM files (stdin/stdout)
+// Provides BAM pipe-specific IO behavior
// ***************************************************************************
#include <api/internal/BamPipe_p.h>
using namespace BamTools::Internal;
#include <cstdio>
+#include <iostream>
using namespace std;
-BamPipe::BamPipe(void)
- : IBamIODevice()
- , m_stream(0)
-{ }
+BamPipe::BamPipe(void) : ILocalIODevice() { }
-BamPipe::~BamPipe(void) {
- Close();
-}
-
-void BamPipe::Close(void) {
-
- // skip if not open
- if ( !IsOpen() ) return;
-
- // flush & close FILE*
- fflush(m_stream);
- fclose(m_stream);
-
- // reset internals
- m_mode = IBamIODevice::NotOpen;
- m_stream = 0;
-}
+BamPipe::~BamPipe(void) { }
bool BamPipe::IsRandomAccess(void) const {
return false;
return true;
}
-size_t BamPipe::Read(char* data, const unsigned int numBytes) {
- BT_ASSERT_X( m_stream, "BamPipe::Read() - null stream" );
- BT_ASSERT_X( (m_mode == IBamIODevice::ReadOnly), "BamPipe::Read() - device not in read-only mode");
- return fread(data, sizeof(char), numBytes, m_stream);
-}
-
bool BamPipe::Seek(const int64_t& position) {
- (void)position; // suppress compiler warning about unused variable
- return false; // seeking not allowed in pipe
-}
+// (void)position; // suppress compiler warning about unused variable
+// return false; // seeking not allowed in pipe
+
+ BT_ASSERT_X( m_stream, "BamFile::Seek() - null stream" );
+ cerr << "BamPipe::Seek() - about to attempt seek" << endl;
+ bool result = ( fseek64(m_stream, position, SEEK_SET) == 0);
+ if ( !result ) {
+ cerr << "BamPipe can't be seeked in" << endl;
+ }
+ return result;
-int64_t BamPipe::Tell(void) const {
- BT_ASSERT_X( m_stream, "BamPipe::Tell() - null stream" );
- return ftell64(m_stream);
-}
+// return ( fseek64(m_stream, position, SEEK_SET) == 0);
-size_t BamPipe::Write(const char* data, const unsigned int numBytes) {
- BT_ASSERT_X( m_stream, "BamPipe::Write() - null stream" );
- BT_ASSERT_X( (m_mode == IBamIODevice::WriteOnly), "BamPipe::Write() - device not in write-only mode" );
- return fwrite(data, sizeof(char), numBytes, m_stream);
}
// ---------------------------------------------------------------------------
// Last modified: 8 September 2011 (DB)
// ---------------------------------------------------------------------------
-// Provides reading/writing of piped BAM files (stdin/stdout)
+// Provides BAM pipe-specific IO behavior
// ***************************************************************************
#ifndef BAMPIPE_P_H
//
// We mean it.
-#include <api/IBamIODevice.h>
+#include <api/internal/ILocalIODevice_p.h>
#include <string>
namespace BamTools {
namespace Internal {
-class BamPipe : public IBamIODevice {
+class BamPipe : public ILocalIODevice {
// ctor & dtor
public:
// IBamIODevice implementation
public:
- void Close(void);
bool IsRandomAccess(void) const;
bool Open(const IBamIODevice::OpenMode mode);
- size_t Read(char* data, const unsigned int numBytes);
bool Seek(const int64_t& position);
- int64_t Tell(void) const;
- size_t Write(const char* data, const unsigned int numBytes);
-
- // internal methods
- private:
-
- // data members
- private:
- FILE* m_stream;
};
} // namespace Internal
// returns BAM file pointer to beginning of alignment data
bool BamReaderPrivate::Rewind(void) {
- if ( !m_stream.IsOpen() )
+ if ( !m_stream.IsOpen() ) {
+ cerr << "BRP::Rewind() - stream not open" << endl;
return false;
+ }
// attempt rewind to first alignment
- if ( !m_stream.Seek(m_alignmentsBeginOffset) )
+ if ( !m_stream.Seek(m_alignmentsBeginOffset) ) {
+ cerr << "BRP::Rewind() - could not seek to ABO (1st time)" << endl;
return false;
+ }
// verify that we can read first alignment
BamAlignment al;
- if ( !LoadNextAlignment(al) )
+ if ( !LoadNextAlignment(al) ) {
+ cerr << "BRP::Rewind() - could not read first alignment" << endl;
return false;
+ }
// reset region
m_randomAccessController.ClearRegion();
#include <api/BamAlignment.h>
#include <api/BamConstants.h>
+#include <api/IBamIODevice.h>
#include <api/internal/BamWriter_p.h>
using namespace BamTools;
using namespace BamTools::Internal;
const RefVector& referenceSequences)
{
// open the BGZF file for writing, return failure if error
- if ( !m_stream.Open(filename, "wb") )
+ if ( !m_stream.Open(filename, IBamIODevice::WriteOnly) )
return false;
// write BAM file 'metadata' components
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() )
+ if ( !IsOpen() /*|| !m_device->IsRandomAccess()*/ ) {
+ cerr << "BgzfStream::Seek() - device not open" << endl;
return false;
+ }
// determine adjusted offset & address
int blockOffset = (position & 0xFFFF);
// attempt seek in file
if ( !m_device->Seek(blockAddress) ) {
- fprintf(stderr, "BgzfStream ERROR: unable to seek in file\n");
+ cerr << "BgzfStream ERROR: unable to seek in file" << endl;
return false;
}
--- /dev/null
+// ***************************************************************************
+// ILocalIODevice_p.cpp (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 8 September 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides shared behavior for files & pipes
+// ***************************************************************************
+
+#include <api/internal/ILocalIODevice_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+using namespace std;
+
+ILocalIODevice::ILocalIODevice(void)
+ : IBamIODevice()
+ , m_stream(0)
+{ }
+
+ILocalIODevice::~ILocalIODevice(void) {
+ Close();
+}
+
+void ILocalIODevice::Close(void) {
+
+ // skip if not open
+ if ( !IsOpen() )
+ return;
+
+ // flush & close FILE*
+ fflush(m_stream);
+ fclose(m_stream);
+
+ // reset internals
+ m_mode = IBamIODevice::NotOpen;
+ m_stream = 0;
+}
+
+size_t ILocalIODevice::Read(char* data, const unsigned int numBytes) {
+ BT_ASSERT_X( m_stream, "ILocalIODevice::Read() - null stream" );
+ BT_ASSERT_X( (m_mode == IBamIODevice::ReadOnly), "ILocalIODevice::Read() - device not in read-only mode");
+ return fread(data, sizeof(char), numBytes, m_stream);
+}
+
+int64_t ILocalIODevice::Tell(void) const {
+ BT_ASSERT_X( m_stream, "ILocalIODevice::Tell() - null stream" );
+ return ftell64(m_stream);
+}
+
+size_t ILocalIODevice::Write(const char* data, const unsigned int numBytes) {
+ BT_ASSERT_X( m_stream, "ILocalIODevice::Write() - null stream" );
+ BT_ASSERT_X( (m_mode == IBamIODevice::WriteOnly), "ILocalIODevice::Write() - device not in write-only mode" );
+ return fwrite(data, sizeof(char), numBytes, m_stream);
+}
--- /dev/null
+// ***************************************************************************
+// ILocalIODevice_p.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 8 September 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides shared behavior for files & pipes
+// ***************************************************************************
+
+#ifndef ILOCALIODEVICE_P_H
+#define ILOCALIODEVICE_P_H
+
+// -------------
+// W A R N I N G
+// -------------
+//
+// This file is not part of the BamTools API. It exists purely as an
+// implementation detail. This header file may change from version to version
+// without notice, or even be removed.
+//
+// We mean it.
+
+#include <api/IBamIODevice.h>
+
+namespace BamTools {
+namespace Internal {
+
+class ILocalIODevice : public IBamIODevice {
+
+ // ctor & dtor
+ public:
+ ILocalIODevice(void);
+ virtual ~ILocalIODevice(void);
+
+ // IBamIODevice implementation
+ public:
+ virtual void Close(void);
+ virtual size_t Read(char* data, const unsigned int numBytes);
+ virtual int64_t Tell(void) const;
+ virtual size_t Write(const char* data, const unsigned int numBytes);
+
+ // data members
+ protected:
+ FILE* m_stream;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // ILOCALIODEVICE_P_H
projects / bamtools.git / commitdiff