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);
}
private static List <CalledAllele> WhatToDoToAlleles(VcfConsumerAppOptions options, T recalibrationData, UpdateSingleAlleleMethod whatToDoWithAllele,
UpdateCoLocatedAllelesMethod whatToDoWithCoLocatedAlleles, List <CalledAllele> variantListFromFile, ref bool updateNeeded)
{
//do any loci-wide actions
var modifiedAsAGroup = new List <CalledAllele>()
{
};
TypeOfUpdateNeeded updateneededForLoci = whatToDoWithCoLocatedAlleles(options, recalibrationData, variantListFromFile, out modifiedAsAGroup);
updateNeeded = (updateneededForLoci != TypeOfUpdateNeeded.NoChangeNeeded);
//do any per-individual allele actions on the new list
var modifiedAsIndividualAlleles = new List <CalledAllele>()
{
};
foreach (var calledAllele in modifiedAsAGroup)
{
var convertedVariants = new List <CalledAllele>()
{
};
TypeOfUpdateNeeded updateneededForAllele = whatToDoWithAllele(options, recalibrationData, calledAllele, out convertedVariants);
updateNeeded = updateNeeded || (updateneededForAllele != TypeOfUpdateNeeded.NoChangeNeeded);
if (updateneededForAllele != TypeOfUpdateNeeded.DeleteCompletely)
{
modifiedAsIndividualAlleles.AddRange(convertedVariants);
}
}
return(modifiedAsIndividualAlleles);
}
/// <summary>
/// This method determines what to actually write out.
/// </summary>
public static TypeOfUpdateNeeded GetTypeOfUpdate(AdaptiveGtOptions options, List <CalledAllele> alleles,
TypeOfUpdateNeeded defaultUpdate, out List <CalledAllele> outGoingAlleles)
{
if (!options.VcfWritingParams.OutputGvcfFile &&
alleles[0].Genotype == Genotype.HomozygousRef ||
alleles[0].Genotype == Genotype.RefLikeNoCall)
{
outGoingAlleles = new List <CalledAllele>(); // Empty list because we don't want to output anything
return(TypeOfUpdateNeeded.DeleteCompletely);
}
else
{
outGoingAlleles = alleles;
return(defaultUpdate);
}
}
/// <summary>
/// Take in a vcf, do stuff to it, write out a vcf. Streamed line by line, loci by loci, so as not to blow up your computer.
/// </summary>
/// <param name="vcfOut"> the output file name</param>
/// <param name="options"> all the parameters associated with writing out a vcf</param>
/// <param name="recalibrationData">the data you need for doing your "stuff" </param>
/// <param name="whatToDoWithSingleAllele">how you want to change each allele</param>
/// <param name="whatToDoWithCoLocatedAlleles">how you want to change each set of alleles, by loci</param>
/// <param name="canSkipLinesWithoutProcessing">when you can skip lines (saves CPU time)</param>
/// <param name="getVcfFileWriter">what your special vcf writer should be, includes special header lines, etc</param>
/// <param name="shouldTrimComplexAlleles">if ACGT-> ACCT is ok, or if you want it trimmed to G -> C. this might affect position and ordering. Generally turn if OFF for processing vcfs, post scylla. </param>
private static void UpdateVcf(string vcfOut, VcfConsumerAppOptions options, bool shouldTrimComplexAlleles, T recalibrationData,
UpdateSingleAlleleMethod whatToDoWithSingleAllele, UpdateCoLocatedAllelesMethod whatToDoWithCoLocatedAlleles,
CanSkipVcfLinesMethod canSkipLinesWithoutProcessing, GetVcfFileWriter getVcfFileWriter)
{
using (AlleleReader reader = new AlleleReader(options.VcfPath, shouldTrimComplexAlleles))
{
using (VcfFileWriter writer = getVcfFileWriter(options, vcfOut))
{
writer.WriteHeader();
writer.FlushBuffer();
var variantListFromFile = new List <CalledAllele>()
{
};
string incomingHangingLine = null;
string outgoingHangingLine = null;
while (true)
{
//get the next group to process
incomingHangingLine = outgoingHangingLine;
var coLocatedVcfLinesToProcess = reader.CloseColocatedLines(incomingHangingLine,
out outgoingHangingLine);
//how we know we are done
if (coLocatedVcfLinesToProcess.Count == 0)
{
break;
}
bool updateNeededForLocus = false;
TypeOfUpdateNeeded updatedNeededForLine = canSkipLinesWithoutProcessing(coLocatedVcfLinesToProcess);
switch (updatedNeededForLine)
{
case TypeOfUpdateNeeded.NoChangeNeeded:
writer.Write(coLocatedVcfLinesToProcess);
break;
case TypeOfUpdateNeeded.Modify:
//then we need to change them into alleles and do stuff to them
variantListFromFile = AlleleReader.VcfLinesToAlleles(coLocatedVcfLinesToProcess);
List <CalledAllele> modifiedVariantListToWrite = WhatToDoToAlleles(options, recalibrationData,
whatToDoWithSingleAllele, whatToDoWithCoLocatedAlleles, variantListFromFile, ref updateNeededForLocus);
if (updateNeededForLocus)
{
writer.Write(modifiedVariantListToWrite);
}
else
{
writer.Write(coLocatedVcfLinesToProcess);
}
break;
case TypeOfUpdateNeeded.DeleteCompletely:
default:
break;
}
}
}
}
}
