public void Dispose()
{
if (_writer != null)
{
_writer.Close();
_writer.Dispose();
_writer = null;
}
}
public void WriteAlignment(BamAlignment alignment)
{
if (alignment == null)
{
_writer?.Dispose();
}
else
{
_writer.WriteAlignment(alignment);
}
}
public void FinishAll()
{
FlushAllBufferedRecords();
_bamWriter.Close();
_bamWriter.Dispose();
using (var writer = GetWriter(_temp2File))
{
AdjustMates(_temp1File, writer);
if (_copyUnaligned)
{
WriteUnalignedReads(writer);
}
}
if (_createIndex)
{
Logger.WriteToLog("Creating index");
new BamIndex().CreateIndexFromBamFile(_temp2File);
Logger.WriteToLog("Completed creating index");
}
// if everything goes well, rename to final destination
File.Delete(_temp1File);
File.Delete(_outputFile);
File.Move(_temp2File, _outputFile);
if (_createIndex)
{
var outputBaiFile = _outputFile + ".bai";
File.Delete(outputBaiFile);
File.Move(_temp2File + ".bai", outputBaiFile);
}
}