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, 100 },
};
foreach (int[] item in SampleValues_ExpectedQScore)
{
var variant = new CalledVariant(AlleleCategory.Snv)
{
Coordinate = 1,
Reference = "A",
Alternate = "T",
TotalCoverage = item[0],
AlleleSupport = item[1],
};
QualityCalculator.Compute(variant, 100, 20);
Assert.Equal(item[2], variant.Qscore);
}
}
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);
}
