private void ProcessVariant(IAlleleSource source, CalledAllele variant)
{
// determine metrics
_coverageCalculator.Compute(variant, source);
if (variant.AlleleSupport > 0)
{
if (_config.NoiseModel == NoiseModel.Window)
{
VariantQualityCalculator.Compute(variant, _config.MaxVariantQscore, (int)MathOperations.PtoQ(variant.SumOfBaseQuality / variant.TotalCoverage));
}
else
{
VariantQualityCalculator.Compute(variant, _config.MaxVariantQscore, _config.EstimatedBaseCallQuality);
}
StrandBiasCalculator.Compute(variant, variant.SupportByDirection, _config.EstimatedBaseCallQuality,
_config.StrandBiasFilterThreshold, _config.StrandBiasModel);
}
// set genotype, filter, etc
AlleleProcessor.Process(variant, _config.MinFrequency, _config.LowDepthFilter,
_config.VariantQscoreFilterThreshold, _config.FilterSingleStrandVariants, _config.VariantFreqFilter, _config.LowGTqFilter, _config.IndelRepeatFilter,
_config.RMxNFilterSettings, _config.ChrReference, source.ExpectStitchedReads);
}
private StrandBiasResults ExecuteTest(Tuple <double, int> forwardStats, Tuple <double, int> reverseStats, Tuple <double, int> stitchedStats,
int estimatedBaseCallQuality = 20, float threshold = 0.5f, StrandBiasModel model = StrandBiasModel.Poisson)
{
var origForwardSupport = (int)(forwardStats.Item1 * forwardStats.Item2);
var origReverseSupport = (int)(reverseStats.Item1 * reverseStats.Item2);
var origStitchedSupport = (int)(stitchedStats.Item1 * stitchedStats.Item2);
var support = new int[]
{
origForwardSupport,
origReverseSupport,
origStitchedSupport,
};
var variant = new CalledVariant(AlleleCategory.Snv)
{
TotalCoverageByDirection = new int[]
{
forwardStats.Item2, reverseStats.Item2, stitchedStats.Item2
}
};
StrandBiasCalculator.Compute(variant, support, estimatedBaseCallQuality, threshold, model);
Assert.Equal(origForwardSupport + ((float)origStitchedSupport / 2), variant.StrandBiasResults.ForwardStats.Support);
Assert.Equal(origReverseSupport + ((float)origStitchedSupport / 2), variant.StrandBiasResults.ReverseStats.Support);
return(variant.StrandBiasResults);
}
private void ProcessVariant(IStateManager source, BaseCalledAllele variant)
{
// determine metrics
CoverageCalculator.Compute(variant, source);
QualityCalculator.Compute(variant, _config.MaxVariantQscore, _config.EstimatedBaseCallQuality);
StrandBiasCalculator.Compute(variant, variant.SupportByDirection, _config.EstimatedBaseCallQuality,
_config.StrandBiasFilterThreshold, _config.StrandBiasModel);
// set genotype, filter, etc
AlleleProcessor.Process(variant, _config.GenotypeModel, _config.MinFrequency, _config.MinCoverage,
_config.VariantQscoreFilterThreshold, _config.FilterSingleStrandVariants);
}
