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); }