public VennProcessor(string[] inputPaths, VennVcfOptions parameters)
{
string outDir = parameters.OutputDirectory;
string consensusFileName = parameters.ConsensusFileName;
_parameters = parameters;
_inputPaths = inputPaths;
_outDir = outDir;
for (int i = 0; i < inputPaths.Length; i++)
{
InputFileNames[i] = Path.GetFileName(inputPaths[i]);
GuessSampleNameFromVcf(InputFileNames[i], out InputSampleNames[i], out InputSampleNums[i]);
}
if (!String.IsNullOrEmpty(consensusFileName))
{
//writeConsensusFile = true;
consensusFilePath = Path.Combine(outDir, consensusFileName);
consensusBuilder = new ConsensusBuilder(consensusFilePath, parameters);
}
}
/// <summary>
/// perfom a Venn split between two samples
/// </summary>
/// <param name="sampleName"></param>
/// <param name="consensusFilePath"></param>
/// <param name="inputPaths"></param>
/// <param name="outputTwoSampleResults"></param>
public void DoPairwiseVenn(bool mFirst)
{
bool doConsensus = (consensusBuilder != null);
bool requireGenotypes = false;
using (VcfReader ReaderA = new VcfReader(_inputPaths[0], requireGenotypes))
using (VcfReader ReaderB = new VcfReader(_inputPaths[1], requireGenotypes))
{
if (doConsensus)
{
consensusBuilder.OpenConsensusFile(ReaderA.HeaderLines);
}
OpenVennDiagramStreams(ReaderA.HeaderLines);
//read the first variant from each gvcf file...
var currentAllele = new CalledAllele();
var backLogPoolAVcfVariant = new VcfVariant();
var backLogPoolBVcfVariant = new VcfVariant();
var backLogExistPoolA = ReaderA.GetNextVariant(backLogPoolAVcfVariant);
var backLogExistPoolB = ReaderB.GetNextVariant(backLogPoolBVcfVariant);
var backLogPoolAAlleles = backLogExistPoolA ? VcfVariantUtilities.Convert(new List <VcfVariant> {
backLogPoolAVcfVariant
}).ToList() : null;
var backLogPoolBAlleles = backLogExistPoolB ? VcfVariantUtilities.Convert(new List <VcfVariant> {
backLogPoolBVcfVariant
}).ToList() : null;
//keep reading and processing until we are done with both gvcfs
while (true)
{
try
{
//1) Get the next set of variants. Pull from the backlog first,
//choosing all the variants at the first available position.
var coLocatedPoolAAlleles = new List <CalledAllele>();
var coLocatedPoolBAlleles = new List <CalledAllele>();
//We need to set up which location to look at next.
//Choose the first one from the backlog.
if (backLogExistPoolA || backLogExistPoolB)
{
if (backLogExistPoolA && backLogExistPoolB)
{
int OrderResult = AlleleCompareByLoci.OrderAlleles(
backLogPoolAAlleles.First(), backLogPoolBAlleles.First(), mFirst);
if (OrderResult < 0)
{
currentAllele.Chromosome = backLogPoolAAlleles.First().Chromosome;
currentAllele.ReferencePosition = backLogPoolAAlleles.First().ReferencePosition;
}
else
{
currentAllele.Chromosome = backLogPoolBAlleles.First().Chromosome;
currentAllele.ReferencePosition = backLogPoolBAlleles.First().ReferencePosition;
}
}
else if (backLogExistPoolB)
{
currentAllele.Chromosome = backLogPoolBAlleles.First().Chromosome;
currentAllele.ReferencePosition = backLogPoolBAlleles.First().ReferencePosition;
}
else //if (backLogExistPoolA)
{
currentAllele.Chromosome = backLogPoolAAlleles.First().Chromosome;
currentAllele.ReferencePosition = backLogPoolAAlleles.First().ReferencePosition;
}
//assemble lists of co-located variants at the position of the current variant
coLocatedPoolAAlleles = AssembleColocatedList(ReaderA, currentAllele, mFirst,
ref backLogExistPoolA, ref backLogPoolAAlleles);
coLocatedPoolBAlleles = AssembleColocatedList(ReaderB, currentAllele, mFirst,
ref backLogExistPoolB, ref backLogPoolBAlleles);
} //else, if there is nothing in either backlog, the colocated-variant list should stay empty.
//2) Now we have finshed reading out all the co-located variants...
//We need organize them into pairs, to know which allele to compare with which.
var Pairs = SelectPairs(coLocatedPoolAAlleles, coLocatedPoolBAlleles);
var ConsensusVariants = new List <CalledAllele>();
AggregateAllele lastConsensusReferenceCall = null;
//3) For each pair, combine them and mark if biased or not.
for (int PairIndex = 0; PairIndex < Pairs.Count; PairIndex++)
{
var VariantA = Pairs[PairIndex][0];
var VariantB = Pairs[PairIndex][1];
var ComparisonCase = GetComparisonCase(VariantA, VariantB);
//add VarA and VarB to appropriate venn diagram files.
WriteVarsToVennFiles(ComparisonCase, VariantA, VariantB);
AggregateAllele Consensus = null;
if (doConsensus)
{
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
//Its possible for multiallelic sites, a pair of variants could
//end up as a concensus reference. And we already may have
//called a reference for this loci already.
//we might have some cleaning up to do...
if (Consensus.Genotype == Pisces.Domain.Types.Genotype.HomozygousRef)
{
//this is the first time we see a reference at this loci
if (lastConsensusReferenceCall == null)
{
lastConsensusReferenceCall = Consensus;
//its OK to fall through and add our Consensus variant to the list.
}
//Else, if we have already called a reference variant
// for this loci already
// we want to merge the results from this reference with the old one.
// *before* we write it to file.
else
{
//the chr, pos, ref, alt,and depth should be correct.
//We'll merge the filters,
//and take the max SB and PB. (where a higher value indicates worse value, so we stay conservative)
lastConsensusReferenceCall.Filters = ConsensusBuilder.CombineFilters(lastConsensusReferenceCall, Consensus);
lastConsensusReferenceCall.StrandBiasResults = new Pisces.Domain.Models.BiasResults()
{
GATKBiasScore = Math.Max(lastConsensusReferenceCall.StrandBiasResults.GATKBiasScore, Consensus.StrandBiasResults.GATKBiasScore)
};
lastConsensusReferenceCall.PoolBiasResults = new Pisces.Domain.Models.BiasResults()
{
GATKBiasScore = Math.Max(lastConsensusReferenceCall.PoolBiasResults.GATKBiasScore, Consensus.PoolBiasResults.GATKBiasScore)
};
//we are going to take the min Q and NL score, to be conservative
lastConsensusReferenceCall.NoiseLevelApplied = Math.Min(lastConsensusReferenceCall.NoiseLevelApplied, Consensus.NoiseLevelApplied);
lastConsensusReferenceCall.GenotypeQscore = Math.Min(lastConsensusReferenceCall.GenotypeQscore, Consensus.GenotypeQscore);
lastConsensusReferenceCall.VariantQscore = Math.Min(lastConsensusReferenceCall.VariantQscore, Consensus.GenotypeQscore);
continue;
}
}
ConsensusVariants.Add(Consensus);
}
}
//4) Write out the results to file. (this will be a list of co-located variants)
if (doConsensus)
{
consensusBuilder.WriteConsensusVariantsToFile(ConsensusVariants);
}
//we assembled everyone and no one is left.
if ((backLogPoolAAlleles == null) &&
(backLogPoolBAlleles == null))
{
break;
}
}
catch (Exception ex)
{
OnError(string.Format("Fatal error encountered comparing paired sample vcfs; Check {0}, position {1}. Exception: {2}",
currentAllele.Chromosome, currentAllele.ReferencePosition, ex));
throw;
}
} //close assemble list
}//close usings
if (doConsensus)
{
consensusBuilder.CloseConsensusFile();
}
CloseVennDiagramStreams();
}
