private static List <MixtureModel> ApplyModels(string vcfIn, string modelFile, List <RecalibratedVariantsCollection> variants)
{
List <MixtureModelParameters> modelParams = MixtureModel.ReadModelsFile(modelFile);
var models = new List <MixtureModel>();
Logger.WriteToLog("Applying models");
for (int i = 0; i < variants.Count; i++)
{
models.Add(MixtureModel.UsePrefitModel(variants[i].Ad, variants[i].Dp, modelParams[i].Means, modelParams[i].Priors));
}
return(models);
}
public void RecalibratedVariantModelAndIndexerTests()
{
var modelsFile = Path.Combine(TestPaths.LocalTestDataDirectory, "example.model");
List <MixtureModelParameters> models = MixtureModel.ReadModelsFile(modelsFile);
var mm = MixtureModel.UsePrefitModel(RecalCollection.Ad, RecalCollection.Dp, models[0].Means, models[0].Priors);
RecalCollection.AddMixtureModelResults(mm);
Assert.Equal(14, RecalCollection.Categories.Count);
Assert.Equal(14, RecalCollection.QScores.Count);
RecalibratedVariant variant1 = RecalCollection["chr1:115252176"];
Assert.Equal(SimplifiedDiploidGenotype.HeterozygousAltRef, variant1.MixtureModelResult.GenotypeCategory);
RecalibratedVariant variant2 = RecalCollection["chr1:115252177"];
Assert.Equal(SimplifiedDiploidGenotype.HomozygousAlt, variant2.MixtureModelResult.GenotypeCategory);
}
private static AdaptiveGenotypingParameters UpdateAdaptiveGenotypingParameters(AdaptiveGenotypingParameters parameters, string inputModelFilePath)
{
if (File.Exists(inputModelFilePath))
{
var newModels = MixtureModel.ReadModelsFile(inputModelFilePath);
parameters.SnvModel = newModels[0].Means;
parameters.SnvPrior = newModels[0].Priors;
parameters.IndelModel = newModels[1].Means;
parameters.IndelPrior = newModels[1].Priors;
}
else
{
throw new ArgumentException("No AdaptiveGT model file found at " + inputModelFilePath);
}
return(parameters);
}
public AdaptiveGtWriterTests()
{
List <MixtureModelParameters> modelParameters = MixtureModel.ReadModelsFile(
Path.Combine(TestPaths.LocalTestDataDirectory, "example.model"));
DefaultResults = new RecalibrationResults
{
SnvResults = new RecalibrationResult
{
Means = modelParameters[0].Means,
Priors = modelParameters[0].Priors,
Variants = new RecalibratedVariantsCollection()
},
IndelResults = new RecalibrationResult
{
Means = modelParameters[1].Means,
Priors = modelParameters[1].Priors,
Variants = new RecalibratedVariantsCollection()
}
};
}
private static List <MixtureModelParameters> ReadAdaptiveGenotypingParametersFromFile(string value)
{
var ListOfMixtureModels = MixtureModel.ReadModelsFile(value);
return(ListOfMixtureModels);
}