// close BAM file
public override void Close()
{
if (!IsOpen)
{
return;
}
IsOpen = false;
_header = "";
_reader.Dispose(); //.net core changes
BgzfFileStream.Dispose(); //.net core changes
}
// close BAM file
public override void Close()
{
if (!IsOpen)
{
return;
}
IsOpen = false;
_header = "";
_reader.Close();
BgzfFileStream.Close();
}
// returns file pointer to beginning of alignments
public void Rewind()
{
BlockLength = 0;
BlockOffset = (int)(_alignmentsOffset & 0xFFFF);
BlockAddress = (_alignmentsOffset >> 16) & 0xFFFFFFFFFFFF;
try
{
BgzfFileStream.Seek(BlockAddress, SeekOrigin.Begin);
}
catch (IOException e)
{
throw new ApplicationException(string.Format("ERROR: Unable to seek in the BAM file: {0}", e.Message));
}
}
// close Bgzipped file
public override void Close()
{
if (!IsOpen)
{
return;
}
IsOpen = false;
// flush the current BGZF block
FlushBlock();
if (_compressQueue != null)
{
// Signal that we're not going to add any more data to the queue.
_compressQueue.CompleteAdding();
// Wait for our compression threads to finish.
int numCompressionThreads = _compressionThreads.Length;
for (int i = 0; i < numCompressionThreads; ++i)
{
_compressionThreads[i].Join();
}
// Signal to the writing thread that compression is complete.
_writeQueue.CompleteAdding();
// Wait for the writing thread to finish.
_writingThread.Join();
}
// write an empty block (as EOF marker)
FlushSingleBlock();
//_writer.Close(); not supported with .net core
//BgzfFileStream.Close();not supported with .net core
_writer.Dispose();
BgzfFileStream.Dispose();
}
