public VariantCaller(CopyNumberLikelihoodCalculator copyNumberLikelihoodCalculator, PedigreeCallerParameters callerParameters, int qualityFilterThreshold)
{
_copyNumberLikelihoodCalculator = copyNumberLikelihoodCalculator;
_callerParameters = callerParameters;
_qualityFilterThreshold = qualityFilterThreshold;
_genotypes = GenerateGenotypeCombinations(callerParameters.MaximumCopyNumber);
}
private static List <List <Genotype> > GetOffspringGenotypes(PedigreeCallerParameters callerParameters, List <Genotype> genotypes, List <SampleId> offspringIds)
{
var offspringGenotypes = new List <List <Genotype> >(Convert.ToInt32(Math.Pow(genotypes.Count, offspringIds.Count)));
GenerateOffspringGenotypes(offspringGenotypes, genotypes, offspringIds.Count, new List <Genotype>());
if (offspringGenotypes.Count > callerParameters.MaxNumOffspringGenotypes)
{
offspringGenotypes.Shuffle();
offspringGenotypes = offspringGenotypes.Take(callerParameters.MaxNumOffspringGenotypes).ToList();
}
return(offspringGenotypes);
}
public CanvasPedigreeCaller(ILogger logger, int qualityFilterThreshold, int deNovoQualityFilterThreshold,
PedigreeCallerParameters callerParameters, CopyNumberLikelihoodCalculator copyNumberLikelihoodCalculator,
IVariantCaller variantCaller, ICoverageBigWigWriter coverageBigWigWriter,
ICopyNumberModelFactory copyNumberModelFactory, ICopyNumberBedGraphWriter copyNumberBedGraphWriter,
CoverageBedGraphWriter partitionCoverageBedGraphWriter)
{
_logger = logger;
_qualityFilterThreshold = qualityFilterThreshold;
_deNovoQualityFilterThreshold = deNovoQualityFilterThreshold;
_callerParameters = callerParameters;
_copyNumberLikelihoodCalculator = copyNumberLikelihoodCalculator;
_variantCaller = variantCaller;
_coverageBigWigWriter = coverageBigWigWriter;
_copyNumberModelFactory = copyNumberModelFactory;
_copyNumberBedGraphWriter = copyNumberBedGraphWriter;
_partitionCoverageBedGraphWriter = partitionCoverageBedGraphWriter;
}
public static PedigreeInfo GetPedigreeInfo(ISampleMap <SampleType> kinships, PedigreeCallerParameters callerParameters)
{
var allSampleIds = kinships.SampleIds.ToReadOnlyList();
bool fullPedigree = kinships.Values.Count(x => x == SampleType.Father) == 1 &&
kinships.Values.Count(x => x == SampleType.Mother) == 1 &&
kinships.Values.Count(x => x == SampleType.Proband) == 1;
// do not populate parents and offspring fields for partial pedigrees
var parentsIds = fullPedigree ? kinships.WhereValues(value => value == SampleType.Father || value == SampleType.Mother).SampleIds.ToList() : new List <SampleId>();
var offspringIds = fullPedigree ? kinships.WhereValues(value => value == SampleType.Proband || value == SampleType.Sibling).SampleIds.ToList() : new List <SampleId>();
var otherIds = fullPedigree ? kinships.WhereValues(value => value == SampleType.Other).SampleIds.ToList() : kinships.SampleIds.ToList();
var parentalPhasedGenotypes = GeneratePhasedGenotype(callerParameters.MaximumCopyNumber);
var parentalTotalCopyNumberGenotypes = Enumerable.Range(0, callerParameters.MaximumCopyNumber).Select(Genotype.Create).ToList();
var offspringPhasedGenotypes = GetOffspringGenotypes(callerParameters, parentalPhasedGenotypes, offspringIds);
var offspringTotalCopyNumberGenotypes = GetOffspringGenotypes(callerParameters, parentalTotalCopyNumberGenotypes, offspringIds);
var transitionMatrix = GetTransitionMatrix(callerParameters.MaximumCopyNumber);
return(new PedigreeInfo(allSampleIds, offspringIds, parentsIds, otherIds, offspringPhasedGenotypes, offspringTotalCopyNumberGenotypes, transitionMatrix));
}
