public static void Recalibrate(SignatureSorterResultFiles countsFilePaths, VQROptions options)
{
string vcfFileName = Path.GetFileName(options.VcfPath);
string vcfOut = Path.Combine(options.OutputDirectory, vcfFileName + ".recal");
if (File.Exists(vcfOut))
{
File.Delete(vcfOut);
}
try
{
//Read in the results files that have the data for the error modes detected.
//Decide which types of variants we want to re-Qscore
var recalibrationData = GetRecalibrationTables(countsFilePaths, options);
//Update Vcf, variant by variant, based on the table data.
VcfUpdater <QualityRecalibrationData> .UpdateVcfAlleleByAllele(vcfOut, options, false, recalibrationData, UpdateAllele, CanSkipVcfLines,
VQRVcfWriter.GetVQRVcfFileWriter);
//let the user know it worked
if (File.Exists(vcfOut))
{
Logger.WriteToLog("The following vcf was recalibrated: " + options.VcfPath);
}
}
catch (Exception ex)
{
Logger.WriteToLog("Recalibrate failed for " + options.VcfPath);
Logger.WriteToLog("Exception: " + ex);
}
}
protected override void ProgramExecution()
{
AdjustOptions(ref _options);
Logger.WriteToLog("Generating counts files");
SignatureSorterResultFiles results = SignatureSorter.StrainVcf(_options);
Logger.WriteToLog("Starting Recalibration");
try
{
QualityRecalibration.Recalibrate(results, _options);
}
catch (Exception e)
{
Logger.WriteToLog("*** Error encountered: {0}", e);
throw e;
}
Logger.WriteToLog("Work complete.");
}
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);
}