private void Call(int?upToPosition = null)
{
var readyBatch = _stateManager.GetCandidatesToProcess(upToPosition, _chrReference);
if (readyBatch == null)
{
return;
}
if (readyBatch.HasCandidates)
{
// evaluate and call variants (including ref calls if producing gvcf)
var BaseCalledAllelesByPosition = _alleleCaller.Call(readyBatch, _stateManager);
var BaseCalledAlleles = BaseCalledAllelesByPosition.Values.SelectMany(a => a).ToList();
// write to vcf
_vcfWriter.Write(BaseCalledAlleles, _regionMapper);
if (_biasFileWriter != null)
{
_biasFileWriter.Write(BaseCalledAlleles);
}
}
if (_intervalSet != null && readyBatch.MaxClearedPosition.HasValue)
{
_intervalSet.SetCleared(readyBatch.MaxClearedPosition.Value);
}
_stateManager.DoneProcessing(readyBatch);
}
private void Call(int?upToPosition = null)
{
var readyBatch = _stateManager.GetCandidatesToProcess(upToPosition, _chrReference);
// map to intervals if needed
if (_regionMapper != null)
{
_regionMapper.Pad(readyBatch, !upToPosition.HasValue);
}
if (readyBatch.HasCandidates)
{
// evaluate and call variants (including ref calls if producing gvcf)
var calledVariants = _alleleCaller.Call(readyBatch, _stateManager);
_numCalledAlleles += calledVariants.Count();
// write to vcf
_vcfWriter.Write(calledVariants);
if (_biasFileWriter != null)
{
_biasFileWriter.Write(calledVariants);
}
}
_stateManager.DoneProcessing(readyBatch);
}
private void Call(int?upToPosition = null)
{
var readyBatch = _stateManager.GetCandidatesToProcess(upToPosition, _chrReference, _forcedGtAlleles);
if (readyBatch == null)
{
return;
}
if (readyBatch.HasCandidates)
{
// evaluate and call variants (including ref calls if producing gvcf)
var BaseCalledAllelesByPosition = _alleleCaller.Call(readyBatch, _stateManager);
var BaseCalledAlleles = BaseCalledAllelesByPosition.Values.SelectMany(a => a).ToList();
// write to vcf
_vcfWriter.Write(BaseCalledAlleles, _regionMapper);
//always coupled together for simplicty, so no need for two checks.
if (_writeBiasFiles)
{
_strandBiasFileWriter.Write(BaseCalledAlleles);
_ampliconBiasFileWriter.Write(BaseCalledAlleles);
}
}
if (_intervalSet != null && readyBatch.MaxClearedPosition.HasValue)
{
_intervalSet.SetCleared(readyBatch.MaxClearedPosition.Value);
}
_stateManager.DoneProcessing(readyBatch);
}