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.");
CanvasSegment.WriteSegments(outFile, this.Segments, referenceFolder, sampleName, null, null);
return 0;
}
PloidyInfo ploidy = null;
if (!string.IsNullOrEmpty(ploidyBedPath)) ploidy = PloidyInfo.LoadPloidyFromBedFile(ploidyBedPath);
// load MAF
this.MeanCoverage = CanvasIO.LoadVariantFrequencies(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.VariantFrequencies) 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);
}
// Merge neighboring segments that got the same copy number call.
CanvasSegment.MergeSegments(ref this.Segments);
CanvasSegment.AssignQualityScores(this.Segments, CanvasSegment.QScoreMethod.LogisticGermline);
List<string> extraHeaders = new List<string>();
string coverageOutputPath = CanvasCommon.Utilities.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);
CanvasSegment.WriteSegments(outFile, this.Segments, referenceFolder, sampleName, extraHeaders, ploidy);
return 0;
}
public int CallVariants(string inFile, string variantFrequencyFile, string outputVCFPath, string referenceFolder, string name, double? localSDmertic)
{
this.OutputFolder = Path.GetDirectoryName(outputVCFPath);
this.TempFolder = Path.GetDirectoryName(inFile);
Console.WriteLine("{0} CallVariants start:", DateTime.Now);
this.Segments = CanvasSegment.ReadSegments(inFile);
// Special logic: Increase the allowed model deviation for targeted data.
if (this.Segments.Count < 500)
this.DeviationFactor = 2.0f;
// Some debugging output, for developer usage:
if (!string.IsNullOrEmpty(this.TruthDataPath))
{
this.CNOracle = new CopyNumberOracle();
this.CNOracle.LoadKnownCN(this.TruthDataPath);
}
if (this.CNOracle != null)
{
this.DebugModelCoverageByCN();
this.DebugModelSegmentCoverageByCN();
}
this.MeanCoverage = CanvasIO.LoadVariantFrequencies(variantFrequencyFile, this.Segments);
if (this.IsDbsnpVcf)
CanvasCommon.Utilities.PruneVariantFrequencies(this.Segments, this.TempFolder, ref MinimumVariantFrequenciesForInformativeSegment);
this.InitializePloidies();
if (this.CNOracle != null) this.DebugModelSegmentsByPloidy();
List<string> ExtraHeaders = new List<string>();
try
{
ExtraHeaders = CallCNVUsingSNVFrequency(localSDmertic, referenceFolder);
string coverageOutputPath = CanvasCommon.Utilities.GetCoverageAndVariantFrequencyOutputPath(outputVCFPath);
CanvasSegment.WriteCoveragePlotData(this.Segments, this.Model.DiploidCoverage, this.ReferencePloidy, coverageOutputPath, referenceFolder);
}
catch (UncallableDataException e)
{
Console.WriteLine("Not calling any CNVs. Reason: {0}", e.Message);
Segments.Clear();
}
if (this.ReferencePloidy != null && !string.IsNullOrEmpty(this.ReferencePloidy.HeaderLine))
{
ExtraHeaders.Add(this.ReferencePloidy.HeaderLine);
}
CanvasSegment.AssignQualityScores(this.Segments, CanvasSegment.QScoreMethod.Logistic);
// Merge *neighboring* segments that got the same copy number call.
// Enrichment is not allowed to merge non-adjacent segments, since many of those merges would
// jump across non-manifest intervals.
if (this.IsEnrichment)
{
CanvasSegment.MergeSegments(ref this.Segments, MinimumCallSize, 1);
}
else
{
CanvasSegment.MergeSegmentsUsingExcludedIntervals(ref this.Segments, MinimumCallSize, ExcludedIntervals);
}
if (this.CNOracle != null)
{
this.DebugEvaluateCopyNumberCallAccuracy();
this.GenerateReportVersusKnownCN();
this.GenerateExtendedReportVersusKnownCN();
}
// Write out results:
CanvasSegment.WriteSegments(outputVCFPath, this.Segments, referenceFolder, name, ExtraHeaders, true, this.ReferencePloidy, true);
return 0;
}