public void SetDerivedParameters(VariantCallingParameters varcallParameters)
{
//SetDerivedParameters these according to ploidy model.
//tjd: I WISH we just never crushed vcfs... Crushing is apparently preffered by germline customers.
if ((varcallParameters.PloidyModel == PloidyModel.DiploidByThresholding) ||
(varcallParameters.PloidyModel == PloidyModel.DiploidByAdaptiveGT))
{
AllowMultipleVcfLinesPerLoci = false;
}
else
{
AllowMultipleVcfLinesPerLoci = true;
}
// override them if desired
if (ForceCrush.HasValue)
{
AllowMultipleVcfLinesPerLoci = !((bool)ForceCrush);
}
//if we have the posteriors data from the adaptive GT model, lets provide it!
if (varcallParameters.PloidyModel == PloidyModel.DiploidByAdaptiveGT)
{
ReportGp = true;
}
}
public void SetDerivedParameters(VariantCallingParameters varcallParameters)
{
//SetDerivedParameters these accoding to ploidy model
if (varcallParameters.PloidyModel == PloidyModel.Diploid)
{
AllowMultipleVcfLinesPerLoci = false;
}
else
{
AllowMultipleVcfLinesPerLoci = true;
}
// override them if desired
if (ForceCrush.HasValue)
{
AllowMultipleVcfLinesPerLoci = !((bool)ForceCrush);
return;
}
}
public static int GetNoiseLevelUsedForQScoring(
VariantCallingParameters varCallingParameters, BamFilterParameters bamFilterParameters)
{
return(varCallingParameters.ForcedNoiseLevel == -1 ? bamFilterParameters.MinimumBaseCallQuality : varCallingParameters.ForcedNoiseLevel);
}