private static QualityRecalibrationData GetRecalibrationTables(SignatureSorterResultFiles resultsFilePaths,
VQROptions options)
{
CountData BasicCounts = null;
CountData EdgeCounts = null;
QualityRecalibrationData recalibrationData = new QualityRecalibrationData();
if (options.DoBasicChecks)
{
if (!File.Exists(resultsFilePaths.BasicCountsFilePath))
{
Logger.WriteToLog("Cannot do basic recalibration. Cannot find {0} ", resultsFilePaths.BasicCountsFilePath);
}
else
{
Logger.WriteToLog("Found counts file: {0} ", resultsFilePaths.BasicCountsFilePath);
BasicCounts = CountsFileReader.ReadCountsFile(resultsFilePaths.BasicCountsFilePath);
recalibrationData.BasicLookupTable = GetPhredScaledCalibratedRates(options.BamFilterParams.MinimumBaseCallQuality, options.ZFactor, BasicCounts);
//if no work to do here...
if ((recalibrationData.BasicLookupTable == null) || (recalibrationData.BasicLookupTable.Count == 0))
{
Logger.WriteToLog("No general recalibration needed.");
}
else
{
Logger.WriteToLog("General mutation bias detected. This sample may have sample-specific prep issues such as FFPE or oxidation damage.");
}
}
}
if (options.DoAmpliconPositionChecks)
{
if (!File.Exists(resultsFilePaths.AmpliconEdgeCountsFilePath))
{
Logger.WriteToLog("Cannot do amplicon-position based recalibration. Cannot find {0} ", resultsFilePaths.AmpliconEdgeCountsFilePath);
}
else
{
Logger.WriteToLog("Found counts file: {0} ", resultsFilePaths.AmpliconEdgeCountsFilePath);
EdgeCounts = CountsFileReader.ReadCountsFile(resultsFilePaths.AmpliconEdgeCountsFilePath);
recalibrationData.AmpliconEdgeVariantsLookupTable = GetPhredScaledCalibratedRates(options.BamFilterParams.MinimumBaseCallQuality, options.ZFactor, EdgeCounts);
recalibrationData.AmpliconEdgeVariantsList = VariantListReader.ReadVariantListFile(resultsFilePaths.AmpliconEdgeSuspectListFilePath);
if ((recalibrationData.AmpliconEdgeVariantsLookupTable == null) || (recalibrationData.AmpliconEdgeVariantsLookupTable.Count == 0))
{
Logger.WriteToLog("No position-in-amplicon recalibration needed.");
}
}
}
//compare edge-issues with FFPE-like issues.
//Did the bulk of variants appear to come from the edge of amplicons..?
//Look at the diff in percents.
//If a variant is X more likely to be called when its by an edge - thats an estimate of the error.
if (options.DoBasicChecks && options.DoAmpliconPositionChecks)
{
recalibrationData.EdgeRiskLookupTable = GetPhredScaledCalibratedRatesForEdges(options.BamFilterParams.MinimumBaseCallQuality, options.AlignmentWarningThreshold, BasicCounts, EdgeCounts);
}
return(recalibrationData);
}
private static TypeOfUpdateNeeded UpdateAllele(VcfConsumerAppOptions appOptions, QualityRecalibrationData recalibrationData, CalledAllele inAllele, out List <CalledAllele> outAlleles)
{
outAlleles = new List <CalledAllele> {
inAllele
};
VQROptions options = (VQROptions)appOptions;
var cat = MutationCounter.GetMutationCategory(inAllele);
TypeOfUpdateNeeded updateHappened = TypeOfUpdateNeeded.NoChangeNeeded;
if (options.DoBasicChecks && recalibrationData.BasicLookupTable.ContainsKey(cat))
{
UpdateVariantQScoreAndRefilter(options.MaxQScore, options.VariantCallingParams.MinimumVariantQScoreFilter, recalibrationData.BasicLookupTable, inAllele, cat, false);
updateHappened = TypeOfUpdateNeeded.Modify;
}
if (options.DoAmpliconPositionChecks &&
recalibrationData.AmpliconEdgeVariantsLookupTable.ContainsKey(cat) &&
recalibrationData.AmpliconEdgeVariantsList.ContainsKey(inAllele.Chromosome) &&
recalibrationData.AmpliconEdgeVariantsList[inAllele.Chromosome].Contains(inAllele.ReferencePosition))
{
UpdateVariantQScoreAndRefilter(options.MaxQScore, options.VariantCallingParams.MinimumVariantQScoreFilter, recalibrationData.EdgeRiskLookupTable, inAllele, cat, true);
updateHappened = TypeOfUpdateNeeded.Modify;
}
return(updateHappened);
}