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.NoiseLevelUsedForQScoring);
}
StrandBiasCalculator.Compute(variant, variant.SupportByDirection, _config.NoiseLevelUsedForQScoring, _config.MinFrequency,
_config.StrandBiasFilterThreshold, _config.StrandBiasModel);
AmpliconBiasCalculator.Compute(variant, _config.MaxVariantQscore, _config.AmpliconBiasFilterThreshold);
}
// set genotype, filter, etc
AlleleProcessor.Process(variant, _config.MinFrequency, _config.LowDepthFilter,
_config.VariantQscoreFilterThreshold, _config.FilterSingleStrandVariants, _config.VariantFreqFilter, _config.LowGTqFilter, _config.IndelRepeatFilter,
_config.RMxNFilterSettings, _config.NoCallFilterThreshold, _config.AmpliconBiasFilterThreshold, _config.ChrReference, source.ExpectStitchedReads);
}
private BiasResultsAcrossAmplicons ExecuteTest(AmpliconCounts supportForAmplicons,
AmpliconCounts coverageForAmplicons, bool expectNull = false)
{
var variant1 = new CalledAllele(AlleleCategory.Snv)
{
SupportByAmplicon = supportForAmplicons,
CoverageByAmplicon = coverageForAmplicons
};
AmpliconBiasCalculator.Compute(variant1, 100, 0.01F);
var variant2 = new CalledAllele(AlleleCategory.Snv)
{
SupportByAmplicon = ReverseAmpliconData(supportForAmplicons),
CoverageByAmplicon = ReverseAmpliconData(coverageForAmplicons)
};
AmpliconBiasCalculator.Compute(variant2, 100, 0.01F);
//sanity check, reversing the input must always give the same result.
if (expectNull)
{
Assert.Null(variant1.AmpliconBiasResults);
Assert.Null(variant2.AmpliconBiasResults);
}
else
{
Assert.Equal(variant1.AmpliconBiasResults.BiasDetected, variant2.AmpliconBiasResults.BiasDetected);
}
return(variant1.AmpliconBiasResults);
}
public void Write()
{
var outFolder = Path.Combine(TestPaths.LocalScratchDirectory, "AmpliconBiasTestOutput");
var outputFile = Path.Combine(outFolder, "AmpliconBiasWriterTests.txt");
TestHelper.RecreateDirectory(outFolder);
//check writing
var chromosome = "chr1";
var reference = "A";
var alternate = "T";
var position = 123;
var BaseCalledAlleles = new List <CalledAllele>();
var variant = new CalledAllele(AlleleCategory.Snv)
{
Chromosome = chromosome,
ReferenceAllele = reference,
AlternateAllele = alternate,
ReferencePosition = position,
SupportByAmplicon = new Domain.Models.AmpliconCounts
{
AmpliconNames = new string[] { "Amplicon1", "Amplicon2", "Amplicon3" },
CountsForAmplicon = new int[] { 12, 4, 5 }
},
CoverageByAmplicon = new Domain.Models.AmpliconCounts
{
AmpliconNames = new string[] { "Amplicon1", "Amplicon2", "Amplicon3" },
CountsForAmplicon = new int[] { 120, 4000, 5000 }
}
};
AmpliconBiasCalculator.Compute(variant, 100, 0.01F);
BaseCalledAlleles.Add(variant);
var writer = new AmpliconBiasFileWriter(outputFile);
writer.WriteHeader();
writer.Write(BaseCalledAlleles);
writer.Dispose();
//check it reads in
//Chr,Position,Reference,Alternate,Name,freq,obs support, expected support, prob its real, confidence Qscore, bias detected ?, Filter Variant?
//chr1,123,A,T,Amplicon1,0.1,12,12,1,100,False,True,
//chr1,123,A,T,Amplicon2,0.001,4,400,2.06343002707725E-165,0,True,True,
//chr1,123,A,T,Amplicon3,0.001,5,500,1.87406134646469E-206,0,True,True,
var biasFileContents = File.ReadAllLines(outputFile);
Assert.True(biasFileContents.Length == 4);
var header = biasFileContents.First();
var expectedHeader = "Chr,Position,Reference,Alternate,Name,freq,obs support, expected support, prob its real, confidence Qscore, bias detected?, Filter Variant?";
var data = biasFileContents.Skip(1).First();
var expectedData = "chr1,123,A,T,Amplicon1,0.1,12,12,1,100,False,True,";
// Make sure well-formed and populated with the right data
Assert.Equal(expectedHeader, header);
Assert.Equal(expectedData, data);
//check IO
Assert.Throws <IOException>(() => writer.WriteHeader());
Assert.Throws <IOException>(() => writer.Write(BaseCalledAlleles));
writer.Dispose();
}