public void Execute()
{
var bamAlignment = new BamAlignment();
int?chrFilterRefIndex = null;
if (_chrFilter != null)
{
chrFilterRefIndex = _bamReader.GetReferenceIndex(_chrFilter);
}
while (true)
{
if (_bufferSize != null && _alignmentBuffer.Count > _bufferSize)
{
FlushToBam();
}
var hasMoreReads = _bamReader.GetNextAlignment(ref bamAlignment, false);
if (!hasMoreReads)
{
break;
}
if (chrFilterRefIndex != null)
{
if (bamAlignment.RefID < chrFilterRefIndex.Value)
{
continue;
}
if (bamAlignment.RefID > chrFilterRefIndex.Value)
{
OnLog("Ending BAM reading for " + _chrFilter + ".");
break;
}
}
if (_getUnpaired && _filter.ReachedFlushingCheckpoint(bamAlignment))
{
var unpaired = _filter.GetFlushableUnpairedReads();
_alignmentBuffer.AddRange(unpaired);
}
var filteredReadPair = _filter.TryPair(bamAlignment);
if (filteredReadPair != null)
{
_alignmentBuffer.AddRange(_pairHandler.ExtractReads(filteredReadPair));
}
}
if (_getUnpaired)
{
var unpaired = _filter.GetFlushableUnpairedReads();
_alignmentBuffer.AddRange(unpaired);
}
FlushToBam();
}
private void FlushUnpaired()
{
if (_unpaired == null)
{
var unpaired = _filter.GetFlushableUnpairedReads();
_unpaired = new Queue <ReadPair>(unpaired.Select(r => new ReadPair(r)));
}
}
public void Execute()
{
var bamAlignment = new BamAlignment();
var bamWriterHandles = _bamWriter.GenerateHandles();
int?chrFilterRefIndex = null;
if (_chrFilter != null)
{
chrFilterRefIndex = _bamReader.GetReferenceIndex(_chrFilter);
}
const int READ_BUFFER_SIZE = 64;
List <ReadPair> readPairBuffer = new List <ReadPair>(READ_BUFFER_SIZE);
while (true)
{
var hasMoreReads = _bamReader.GetNextAlignment(ref bamAlignment, false);
if (!hasMoreReads)
{
break;
}
if (chrFilterRefIndex != null)
{
if (bamAlignment.RefID < chrFilterRefIndex.Value)
{
continue;
}
if (bamAlignment.RefID > chrFilterRefIndex.Value)
{
Logger.WriteToLog("Ending BAM reading for " + _chrFilter + ".");
break;
}
}
if (_getUnpaired && _filter.ReachedFlushingCheckpoint(bamAlignment))
{
ExecuteTask(new FlushableUnpairedReadsTask(_filter.GetFlushableUnpairedReads(), bamWriterHandles));
}
var filteredReadPair = _filter.TryPair(bamAlignment);
if (filteredReadPair != null)
{
readPairBuffer.Add(filteredReadPair);
if (readPairBuffer.Count >= READ_BUFFER_SIZE - 1)
{
ExecuteTask(new ExtractReadsTask(_pairHandlers, readPairBuffer, bamWriterHandles, _filter));
readPairBuffer = new List <ReadPair>(READ_BUFFER_SIZE);
}
}
}
if (readPairBuffer.Count > 0)
{
ExecuteTask(new ExtractReadsTask(_pairHandlers, readPairBuffer, bamWriterHandles, _filter));
}
if (_getUnpaired)
{
ExecuteTask(new FlushableUnpairedReadsTask(_filter.GetFlushableUnpairedReads(), bamWriterHandles));
}
WaitForFinishTask.WaitUntilZeroTasks();
}