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();
}
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();
}
public ReadPair GetNextEntryUntilNull()
{
var bamAlignment = new BamAlignment();
while (!_hasPassedChrom)
{
bool hasMoreReads;
hasMoreReads = _bamReader.GetNextAlignment(ref bamAlignment, false);
if (!hasMoreReads || _applyChrFilter && bamAlignment.RefID > _refId)
{
FlushUnpaired();
if (_applyChrFilter && bamAlignment.RefID > _refId)
{
_hasPassedChrom = true;
}
break;
}
if (_applyChrFilter && bamAlignment.RefID < _refId)
{
AddStatus(TooLow);
continue;
}
if (bamAlignment.IsDuplicate() && _skipAndRemoveDuplicates)
{
AddStatus(Duplicate);
continue;
}
// TODO did we want to handle secondary/supplementaries differently?
//if (bamAlignment.IsSecondary() || !bamAlignment.IsPrimaryAlignment())
//{
// continue;
//}
if (ShouldSkipRead(bamAlignment))
{
continue;
}
var status = SingleReadStatus(bamAlignment);
if (status != PairStatus.Unknown)
{
AddStatus(WontPair);
return(new ReadPair(bamAlignment)
{
PairStatus = status
});
}
var filteredReadPair = _filter.TryPair(bamAlignment, status);
if (filteredReadPair != null)
{
if (filteredReadPair.PairStatus != PairStatus.OffTarget)
{
filteredReadPair.PairStatus = PairStatus.Paired;
}
return(filteredReadPair);
}
}
while (true)
{
if (_unpaired == null || !_unpaired.Any())
{
break;
}
return(_unpaired.Dequeue());
}
return(null);
}