public static void Process(BaseCalledAllele allele, GenotypeModel model,
float minFrequency, int minCoverage, int?filterVariantQscore, bool filterSingleStrandVariants)
{
SetFractionNoCall(allele);
ApplyFilters(allele, minCoverage, filterVariantQscore, filterSingleStrandVariants);
SetGenotype(allele, model, minFrequency);
}
private static void SetGenotype(BaseCalledAllele allele, GenotypeModel model, float minFrequency)
{
if (allele.Filters.Contains(FilterType.LowDepth))
{
allele.Genotype = allele is CalledReference ? Genotype.RefLikeNoCall : Genotype.AltLikeNoCall;
}
else if (allele is CalledVariant && model != GenotypeModel.None)
{
var variant = (CalledVariant)allele;
// if we see no evidence of a reference allele, according to the genotype model
// then presume our variant is a homozygous alt
if (variant.RefFrequency < (model == GenotypeModel.Symmetrical ? minFrequency : 0.25f))
{
//if we are using the thresholding model, if we see less than 25% reference,
variant.Genotype = Genotype.HomozygousAlt;
}
}
}
public ApplicationOptions UpdateOptions(string[] arguments)
{
string lastArgumentField = string.Empty;
try
{
int argumentIndex = 0;
while (argumentIndex < arguments.Length)
{
if (arguments[argumentIndex] == null || arguments[argumentIndex].Length == 0)
{
argumentIndex++;
continue;
}
string value = null;
if (argumentIndex < arguments.Length - 1)
{
value = arguments[argumentIndex + 1];
}
lastArgumentField = arguments[argumentIndex];
switch (lastArgumentField)
{
case "-a":
MinimumVariantQScore = int.Parse(value);
break;
case "-b":
MinimumBaseCallQuality = int.Parse(value);
break;
case "-B":
BAMPaths = value.Split(_delimiter);
break;
case "-BAMFolder":
BAMFolder = value;
break;
case "-c":
MinimumCoverage = int.Parse(value);
break;
case "-d":
DebugMode = bool.Parse(value);
break;
case "-debug":
DebugMode = bool.Parse(value);
break;
case "-f":
MinimumFrequency = float.Parse(value);
break;
case "-F":
FilteredVariantQScore = int.Parse(value);
break;
case "-fo":
FilterOutVariantsPresentOnlyOneStrand = bool.Parse(value);
break;
case "-g":
GenomePaths = value.Split(_delimiter);
break;
case "-NL":
AppliedNoiseLevel = int.Parse(value);
break;
case "-gVCF":
OutputgVCFFiles = bool.Parse(value);
break;
case "-CallMNVs":
case "-PhaseSNPs":
CallMNVs = bool.Parse(value);
break;
case "-MaxMNVLength":
case "-MaxPhaseSNPLength":
MaxSizeMNV = int.Parse(value);
break;
case "-MaxGapBetweenMNV":
case "-MaxGapPhasedSNP":
MaxGapBetweenMNV = int.Parse(value);
break;
case "-i":
IntervalPaths = value.Split(_delimiter);
break;
case "-m":
MinimumMapQuality = int.Parse(value);
break;
case "-GT":
if (value.ToLower().Contains("none"))
{
GTModel = GenotypeModel.None;
}
else if (value.ToLower().Contains("threshold"))
{
GTModel = GenotypeModel.Thresholding;
}
else if (value.ToLower().Contains("symmetric"))
{
GTModel = GenotypeModel.Symmetrical;
}
else
{
throw new ArgumentException(string.Format("Unknown genotype model '{0}'", value));
}
break;
case "-SBModel":
if (value.ToLower().Contains("poisson"))
{
StrandBiasModel = StrandBiasModel.Poisson;
}
else if (value.ToLower().Contains("extended"))
{
StrandBiasModel = StrandBiasModel.Extended;
}
else
{
throw new ArgumentException(string.Format("Unknown strand bias model '{0}'", value));
}
break;
case "-o":
OutputBiasFiles = bool.Parse(value);
break;
case "-p":
OnlyUseProperPairs = bool.Parse(value);
break;
case "-q":
MaximumVariantQScore = int.Parse(value);
break;
case "-s":
StrandBiasAcceptanceCriteria = float.Parse(value);
break;
case "-StitchPairedReads":
StitchReads = bool.Parse(value);
break;
case "-t":
MaxNumThreads = int.Parse(value);
break;
case "-ThreadByChr":
ThreadByChr = bool.Parse(value);
break;
case "-ReportNoCalls":
ReportNoCalls = bool.Parse(value);
break;
case "-requireXC":
RequireXCTagToStitch = bool.Parse(value);
break;
case "-xcStitcher":
UseXCStitcher = bool.Parse(value);
break;
case "-OutFolder":
OutputFolder = value;
break;
default:
throw new Exception(string.Format("Unknown argument '{0}'", arguments[argumentIndex]));
}
argumentIndex += 2;
}
CommandLineArguments = string.Join(" ", arguments);
return(this);
}
catch (Exception ex)
{
if (string.IsNullOrEmpty(lastArgumentField))
{
throw new Exception("Unable to parse arguments: " + ex.Message);
}
throw new Exception(string.Format("Unable to parse argument {0}: {1}", lastArgumentField, ex.Message));
}
}
private void ExecuteGenotypeTest(int totalCoverage, float refFrequency, bool isReference, GenotypeModel model, Genotype expectedGenotype)
{
var variant = CreatePassingVariant(isReference);
variant.TotalCoverage = totalCoverage;
if (!isReference)
{
var refSupport = (int)(refFrequency * totalCoverage);
variant.AlleleSupport = totalCoverage - refSupport;
((CalledVariant)variant).ReferenceSupport = refSupport;
}
AlleleProcessor.Process(variant, model, 0.01f, 100, 20, false);
Assert.Equal(expectedGenotype, variant.Genotype);
}
