public int CallVariants(string variantFrequencyFile, string inFile, string outFile, string ploidyBedPath, string referenceFolder, string sampleName,
string truthDataPath)
{
if (!string.IsNullOrEmpty(truthDataPath))
{
this.CNOracle = new CopyNumberOracle();
this.CNOracle.LoadKnownCN(truthDataPath);
}
this.Segments = CanvasSegment.ReadSegments(inFile);
this.TempFolder = Path.GetDirectoryName(inFile);
if (this.Segments.Count == 0)
{
Console.WriteLine("CanvasDiploidCaller: No segments loaded; no CNV calls will be made.");
CanvasSegmentWriter.WriteSegments(outFile, this.Segments, Model?.DiploidCoverage, referenceFolder,
sampleName, null, null, QualityFilterThreshold, isPedigreeInfoSupplied: false);
return(0);
}
PloidyInfo ploidy = null;
if (!string.IsNullOrEmpty(ploidyBedPath))
{
ploidy = PloidyInfo.LoadPloidyFromBedFile(ploidyBedPath);
}
// load MAF
this.MeanCoverage = CanvasIO.LoadFrequencies(variantFrequencyFile, this.Segments);
int medianVariantCoverage = AggregateVariantCoverage(ref this.Segments);
// Create new models for different copy number states
this.InitializePloidies();
// Compute statistics on the copy number two regions
float[] diploidCounts = AggregateCounts(ref this.Segments);
DiploidCoverage = CanvasCommon.Utilities.Mean(diploidCounts);
CoverageWeightingFactor = CoverageWeighting / DiploidCoverage;
// new coverage model
this.Model = new CoverageModel();
Model.DiploidCoverage = DiploidCoverage;
List <SegmentInfo> segments = new List <SegmentInfo>();
foreach (CanvasSegment segment in this.Segments)
{
SegmentInfo info = new SegmentInfo();
info.Segment = segment;
List <double> MAF = new List <double>();
foreach (float value in segment.Alleles.Frequencies)
{
MAF.Add(value > 0.5 ? 1 - value : value);
}
if (MAF.Count > 0)
{
info.MAF = CanvasCommon.Utilities.Median(MAF);
}
else
{
info.MAF = -1;
}
info.Coverage = CanvasCommon.Utilities.Median(segment.Counts);
if (this.Segments.Count > 100)
{
info.Weight = segment.End - segment.Begin;
}
else
{
info.Weight = segment.BinCount;
}
segments.Add(info);
}
// Assign copy number and major chromosome count for each segment
bool useGaussianMixtureModel = false; // For now, this is set false, since we saw weird performance on chrY (CANV-115):
if (useGaussianMixtureModel)
{
// optimize model covariance
double likelihood = FitGaussians(Model, segments);
AssignPloidyCallsGaussianMixture();
}
else
{
AssignPloidyCallsDistance(Model, segments, medianVariantCoverage);
}
CanvasSegment.AssignQualityScores(this.Segments, CanvasSegment.QScoreMethod.LogisticGermline, germlineScoreParameters);
// Merge neighboring segments that got the same copy number call.
// merging segments requires quality scores so we do it after quality scores have been assigned
CanvasSegment.MergeSegments(ref this.Segments);
// recalculating qscores after merging segments improves performance!
CanvasSegment.AssignQualityScores(this.Segments, CanvasSegment.QScoreMethod.LogisticGermline, germlineScoreParameters);
CanvasSegment.FilterSegments(QualityFilterThreshold, Segments);
List <string> extraHeaders = new List <string>();
string coverageOutputPath = SingleSampleCallset.GetCoverageAndVariantFrequencyOutputPath(outFile);
CanvasSegment.WriteCoveragePlotData(this.Segments, Model.DiploidCoverage, ploidy, coverageOutputPath, referenceFolder);
if (this.CNOracle != null)
{
this.GenerateReportVersusKnownCN();
}
if (ploidy != null && !string.IsNullOrEmpty(ploidy.HeaderLine))
{
extraHeaders.Add(ploidy.HeaderLine);
}
CanvasSegmentWriter.WriteSegments(outFile, this.Segments, Model.DiploidCoverage, referenceFolder, sampleName,
extraHeaders, ploidy, QualityFilterThreshold, isPedigreeInfoSupplied: false);
return(0);
}