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);
}
public void Compute()
{
// Based on Tamsen's original PValue test, just extended to our Compute method
List <int[]> SampleValues_ExpectedQScore = new List <int[]>() //coverage,var calls}
{
new int[] { 100, 0, 0 },
new int[] { 100, 1, 2 },
new int[] { 100, 5, 24 },
new int[] { 200, 10, 43 },
new int[] { 500, 25, 98 },
new int[] { 5000, 250, 890 },
new int[] { 10000, 250, 356 },
new int[] { 10000, 500, 1770 },
new int[] { 10000, 9995, 156912 }, //ok, this is a silly number. but we are checking the range..
};
foreach (int[] item in SampleValues_ExpectedQScore)
{
var variant = new CalledAllele(AlleleCategory.Snv)
{
ReferencePosition = 1,
ReferenceAllele = "A",
AlternateAllele = "T",
TotalCoverage = item[0],
AlleleSupport = item[1],
};
VariantQualityCalculator.Compute(variant, int.MaxValue, 20);
Assert.Equal(item[2], variant.VariantQscore);
//check upped bd works:
VariantQualityCalculator.Compute(variant, 100, 20);
Assert.Equal(Math.Min(100, item[2]), variant.VariantQscore);
}
}
