public static SampleMetrics GetSampleInfo(IReadOnlyList <CanvasSegment> segments, string ploidyBedPath, int numberOfTrimmedBins, SampleId id)
{
double meanMafCoverage = new SortedList <int>(segments.SelectMany(x => x.Balleles.TotalCoverage)).Median();
double variance = Utilities.Variance(segments.Select(x => x.TruncatedMedianCount(numberOfTrimmedBins)).ToList());
double mafVariance = Utilities.Variance(segments.Where(x => x.Balleles.TotalCoverage.Count > 0)
.Select(x => x.Balleles.TotalCoverage.Average()).ToList());
double meanCoverage = new SortedList <float>(segments.SelectMany(x => x.Counts).Select(x => x)).Median();
int maxCoverage = Convert.ToInt16(segments.Select(x => x.TruncatedMedianCount(numberOfTrimmedBins)).Max()) + 10;
var ploidy = new PloidyInfo();
if (!ploidyBedPath.IsNullOrEmpty() && File.Exists(ploidyBedPath))
{
ploidy = PloidyInfo.LoadPloidyFromVcfFile(ploidyBedPath, id.ToString());
}
return(new SampleMetrics(meanCoverage, meanMafCoverage, variance, mafVariance, maxCoverage, ploidy));
}
internal int CallVariants(List <string> variantFrequencyFiles, List <string> segmentFiles,
IFileLocation outVcfFile, string ploidyBedPath, string referenceFolder, List <string> sampleNames, string commonCnvsBedPath, List <SampleType> sampleTypes)
{
// load files
// initialize data structures and classes
var fileCounter = 0;
var samplesInfo = new SampleMap <SampleMetrics>();
var sampleSegments = new SampleMap <Segments>();
var copyNumberModels = new SampleMap <ICopyNumberModel>();
var variantFrequencyFilesSampleList = new SampleMap <string>();
var kinships = new SampleMap <SampleType>();
foreach (string sampleName in sampleNames)
{
var sampleId = new SampleId(sampleName);
var segment = Segments.ReadSegments(_logger, new FileLocation(segmentFiles[fileCounter]));
segment.AddAlleles(CanvasIO.ReadFrequenciesWrapper(_logger, new FileLocation(variantFrequencyFiles[fileCounter]), segment.IntervalsByChromosome));
sampleSegments.Add(sampleId, segment);
var sampleInfo = SampleMetrics.GetSampleInfo(segment.AllSegments, ploidyBedPath, _callerParameters.NumberOfTrimmedBins, sampleId);
var copyNumberModel = _copyNumberModelFactory.CreateModel(_callerParameters.MaximumCopyNumber, sampleInfo.MaxCoverage, sampleInfo.MeanCoverage, sampleInfo.MeanMafCoverage);
samplesInfo.Add(sampleId, sampleInfo);
copyNumberModels.Add(sampleId, copyNumberModel);
variantFrequencyFilesSampleList.Add(sampleId, variantFrequencyFiles[fileCounter]);
kinships.Add(sampleId, sampleTypes[fileCounter]);
fileCounter++;
}
var segmentSetsFromCommonCnvs = CreateSegmentSetsFromCommonCnvs(variantFrequencyFilesSampleList,
_callerParameters.MinAlleleCountsThreshold, commonCnvsBedPath, sampleSegments);
var segmentsForVariantCalling = GetHighestLikelihoodSegments(segmentSetsFromCommonCnvs, samplesInfo, copyNumberModels).ToList();
PedigreeInfo pedigreeInfo = PedigreeInfo.GetPedigreeInfo(kinships, _callerParameters);
Parallel.ForEach(
segmentsForVariantCalling,
new ParallelOptions
{
MaxDegreeOfParallelism = Math.Min(Environment.ProcessorCount, _callerParameters.MaxCoreNumber)
},
segments => _variantCaller.CallVariant(segments, samplesInfo, copyNumberModels, pedigreeInfo)
);
var variantCalledSegments = new SampleMap <List <CanvasSegment> >();
foreach (var key in samplesInfo.SampleIds)
{
variantCalledSegments.Add(key, segmentsForVariantCalling.Select(segment => segment[key]).ToList());
}
var mergedVariantCalledSegments = MergeSegments(variantCalledSegments, _callerParameters.MinimumCallSize, _qualityFilterThreshold);
FilterExcessivelyShortSegments(mergedVariantCalledSegments);
var outputFolder = outVcfFile.Directory;
foreach (var sampleId in samplesInfo.SampleIds)
{
var coverageOutputPath = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(outputFolder,
sampleId.ToString());
CanvasSegment.WriteCoveragePlotData(mergedVariantCalledSegments[sampleId], samplesInfo[sampleId].MeanCoverage,
samplesInfo[sampleId].Ploidy, coverageOutputPath, referenceFolder);
}
bool isPedigreeInfoSupplied = pedigreeInfo != null && pedigreeInfo.HasFullPedigree();
var denovoQualityThreshold = isPedigreeInfoSupplied ? (int?)_deNovoQualityFilterThreshold : null;
var ploidies = samplesInfo.Select(info => info.Value.Ploidy).ToList();
var diploidCoverage = samplesInfo.Select(info => info.Value.MeanCoverage).ToList();
var names = samplesInfo.SampleIds.Select(id => id.ToString()).ToList();
CanvasSegmentWriter.WriteMultiSampleSegments(outVcfFile.FullName, mergedVariantCalledSegments, diploidCoverage, referenceFolder, names,
null, ploidies, _qualityFilterThreshold, denovoQualityThreshold, CanvasFilter.SegmentSizeCutoff, isPedigreeInfoSupplied);
foreach (var sampleId in samplesInfo.SampleIds)
{
var outputVcfPath = SingleSampleCallset.GetVcfOutput(outputFolder, sampleId.ToString());
var sampleMetrics = samplesInfo[sampleId];
var segments = mergedVariantCalledSegments[sampleId];
CanvasSegmentWriter.WriteSegments(outputVcfPath.FullName, segments,
sampleMetrics.MeanCoverage, referenceFolder, sampleId.ToString(), null,
sampleMetrics.Ploidy, _qualityFilterThreshold, isPedigreeInfoSupplied, denovoQualityThreshold, null);
var visualizationTemp = outputFolder.CreateSubdirectory($"VisualizationTemp{sampleId}");
var normalizationFactor = NormalizationCalculator.ComputeNormalizationFactor(segments);
var bigWig = _coverageBigWigWriter.Write(segments, visualizationTemp, normalizationFactor);
bigWig?.MoveTo(SingleSampleCallset.GetCoverageBigWig(outputFolder, sampleId.ToString()));
var copyNumberBedGraph = SingleSampleCallset.GetCopyNumberBedGraph(outputFolder, sampleId.ToString());
_copyNumberBedGraphWriter.Write(segments, sampleMetrics.Ploidy, copyNumberBedGraph);
var partitionBedgraphHeader = "track type=bedGraph visibility=full autoScale=on graphType=points";
var originalSegments = sampleSegments[sampleId];
_partitionCoverageBedGraphWriter.Write(originalSegments.AllSegments, SingleSampleCallset.GetPartitionBedGraph(outputFolder, sampleId.ToString()), normalizationFactor, partitionBedgraphHeader);
}
return(0);
}