/// <summary>
/// Given a set canvasSegmentsSet with two alternative segmentation hypothesis (SegmentsSet: SetA and SetB), return log likelihood
/// for a segmentation hypothesis specified by segmentsSet. Segmentation hypothesis could typically include segmentation results specified
/// by partitioning or annotations of population (common) variants
/// </summary>
/// <param name="canvasSegmentsSet"></param>
/// <param name="samplesInfo"></param>
/// <param name="copyNumberModel"></param>
/// <param name="segmentsSet"></param>
/// <returns></returns>
private double GetSegmentSetLogLikelihood(ISampleMap <OverlappingSegmentsRegion> canvasSegmentsSet, ISampleMap <SampleMetrics> samplesInfo,
ISampleMap <ICopyNumberModel> copyNumberModel, SegmentsSet segmentsSet)
{
double segmentSetLogLikelihood = 0;
foreach (var sampleId in canvasSegmentsSet.SampleIds)
{
canvasSegmentsSet[sampleId].SetSet(segmentsSet);
}
var canvasSegments = new List <ISampleMap <CanvasSegment> >();
int nSegments = canvasSegmentsSet.First().Value.GetSet().Count;
for (var canvasSegmentIndex = 0; canvasSegmentIndex < nSegments; canvasSegmentIndex++)
{
var canvasSegment = new SampleMap <CanvasSegment>();
foreach (var id in canvasSegmentsSet.SampleIds)
{
canvasSegment.Add(id, canvasSegmentsSet[id].GetSet()[canvasSegmentIndex]);
}
canvasSegments.Add(canvasSegment);
}
foreach (var canvasSegment in canvasSegments)
{
var copyNumbersLikelihoods = _copyNumberLikelihoodCalculator.GetCopyNumbersLikelihoods(canvasSegment, samplesInfo, copyNumberModel, _callerParameters.NumberOfTrimmedBins);
var(_, likelihoods) = GetCopyNumbersNoPedigreeInfo(canvasSegment, copyNumbersLikelihoods);
segmentSetLogLikelihood += likelihoods.MaximalLogLikelihood;
}
return(segmentSetLogLikelihood);
}
/// <summary>
/// Identify variant with the highest likelihood at a given setPosition and assign relevant scores
/// </summary>
public void CallVariant(ISampleMap <CanvasSegment> canvasSegments, ISampleMap <SampleMetrics> samplesInfo,
ISampleMap <ICopyNumberModel> copyNumberModel, PedigreeInfo pedigreeInfo)
{
var singleSampleLikelihoods = _copyNumberLikelihoodCalculator.GetCopyNumbersLikelihoods(canvasSegments, samplesInfo, copyNumberModel, _callerParameters.NumberOfTrimmedBins);
(var pedigreeCopyNumbers, var pedigreeLikelihoods) = GetPedigreeCopyNumbers(pedigreeInfo, singleSampleLikelihoods);
var nonPedigreeCopyNumbers = CanvasPedigreeCaller.GetNonPedigreeCopyNumbers(canvasSegments, pedigreeInfo, singleSampleLikelihoods);
var mergedCopyNumbers = pedigreeCopyNumbers.Concat(nonPedigreeCopyNumbers).OrderBy(canvasSegments.SampleIds);
EstimateQScores(canvasSegments, samplesInfo, pedigreeInfo, singleSampleLikelihoods, pedigreeLikelihoods, mergedCopyNumbers);
// TODO: this will be integrated with GetCopyNumbers* on a model level as a part of https://jira.illumina.com/browse/CANV-404
if (CanvasPedigreeCaller.UseAlleleCountsInformation(canvasSegments, _callerParameters.MinAlleleCountsThreshold, _callerParameters.MinAlleleNumberInSegment) &&
pedigreeInfo.HasFullPedigree())
{
AssignMccWithPedigreeInfo(canvasSegments, copyNumberModel, pedigreeInfo);
}
if (CanvasPedigreeCaller.UseAlleleCountsInformation(canvasSegments, _callerParameters.MinAlleleCountsThreshold, _callerParameters.MinAlleleNumberInSegment) &&
pedigreeInfo.HasOther())
{
AssignMccNoPedigreeInfo(canvasSegments.Where(segment => pedigreeInfo.OtherIds.Contains(segment.SampleId)).ToSampleMap(), copyNumberModel, _genotypes);
}
}
public void CallVariant(ISampleMap <CanvasSegment> canvasSegments, ISampleMap <SampleMetrics> samplesInfo,
ISampleMap <ICopyNumberModel> copyNumberModel, PedigreeInfo pedigreeInfo)
{
var coverageLikelihoods = _copyNumberLikelihoodCalculator.GetCopyNumbersLikelihoods(canvasSegments, samplesInfo, copyNumberModel);
// if number and properties of SNPs in the segment are above threshold, calculate likelihood from SNPs and merge with
// coverage likelihood to form merged likelihoods
int nBalleles = canvasSegments.Values.First().Balleles.Size();
// If allele information is available (i.e. segment has enough SNPs) merge coverage and allele likelihood obtained by GetGenotypeLogLikelihoods
// into singleSampleLikelihoods using JoinLikelihoods function.
var singleSampleLikelihoods = CanvasPedigreeCaller.UseAlleleCountsInformation(canvasSegments,
_callerParameters.MinAlleleCountsThreshold, _callerParameters.MinAlleleNumberInSegment)
? JoinLikelihoods(GetGenotypeLogLikelihoods(canvasSegments, copyNumberModel, _PhasedGenotypes), coverageLikelihoods, nBalleles)
: ConvertToLogLikelihood(coverageLikelihoods);
// estimate joint likelihood across pedigree samples from singleSampleLikelihoods using either only coverage or coverage + allele counts
(var pedigreeCopyNumbers, var pedigreeLikelihoods) = GetPedigreeCopyNumbers(pedigreeInfo, singleSampleLikelihoods);
var nonPedigreeCopyNumbers = CanvasPedigreeCaller.GetNonPedigreeCopyNumbers(canvasSegments, pedigreeInfo, singleSampleLikelihoods);
var mergedCopyNumbers = nonPedigreeCopyNumbers.Concat(pedigreeCopyNumbers).OrderBy(canvasSegments.SampleIds);
AssignCNandScores(canvasSegments, samplesInfo, pedigreeInfo, singleSampleLikelihoods,
pedigreeLikelihoods, mergedCopyNumbers);
}