#include <api/BamAlignment.h>
#include <api/BamConstants.h>
+<<<<<<< HEAD
#include <api/internal/BamException_p.h>
+=======
+#include <api/IBamIODevice.h>
+>>>>>>> iodevice
#include <api/internal/BamWriter_p.h>
using namespace BamTools;
using namespace BamTools::Internal;
// returns whether BAM file is open for writing or not
bool BamWriterPrivate::IsOpen(void) const {
- return m_stream.IsOpen;
+ return m_stream.IsOpen();
}
// opens the alignment archive
const string& samHeaderText,
const RefVector& referenceSequences)
{
+<<<<<<< HEAD
try {
+=======
+ // open the BGZF file for writing, return failure if error
+ if ( !m_stream.Open(filename, IBamIODevice::WriteOnly) )
+ return false;
+>>>>>>> iodevice
// open the BGZF file for writing, return failure if error
m_stream.Open(filename, "wb");