// BamFile_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
-// Provides reading of local BAM files
+// Provides BAM file-specific IO behavior
// ***************************************************************************
-#include <api/internal/BamFile_p.h>
+#include "api/internal/BamFile_p.h"
using namespace BamTools;
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 {
else if ( mode == IBamIODevice::WriteOnly )
m_stream = fopen(m_filename.c_str(), "wb");
else {
- SetErrorString("BamFile ERROR - unknown device open mode");
+ SetErrorString("BamFile::Open", "unknown open mode requested");
return false;
}
// check that we obtained a valid FILE*
if ( m_stream == 0 ) {
- string error = "BamFile ERROR - could not open handle on ";
- error += ( (m_filename.empty()) ? "empty filename" : m_filename );
- SetErrorString(error);
+ const string message_base = string("could not open file handle for ");
+ const string message = message_base + ( (m_filename.empty()) ? "empty filename" : m_filename );
+ SetErrorString("BamFile::Open", message);
return false;
}
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" );
- 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);
+ return ( fseek64(m_stream, position, SEEK_SET) == 0 );
}