public VcfNeighborhoodBuilder(PhasableVariantCriteria phasableVariantCriteria, VariantCallingParameters variantCallingParams, IVcfVariantSource vcfVariantSource) { _chrsToProcess = phasableVariantCriteria.ChrToProcessArray; _passingOnly = phasableVariantCriteria.PassingVariantsOnly; _hetOnly = phasableVariantCriteria.HetVariantsOnly; _phasingDistance = phasableVariantCriteria.PhasingDistance; _vcfVariantSource = vcfVariantSource; _neighborhoods = new List <VcfNeighborhood>(); _variantCallingParams = variantCallingParams; }
public VcfNeighborhoodBuilder(PhasableVariantCriteria phasableVariantCriteria, VariantCallingParameters variantCallingParams, IVcfVariantSource vcfVariantSource, int batchSize) { _variantCallingParams = variantCallingParams; _phasableVariantCriteria = phasableVariantCriteria; _vcfVariantSource = vcfVariantSource; _nextBatchOfNeighborhoods = new List <VcfNeighborhood>(); _unfinshedNeighborhoods = new List <VcfNeighborhood>(); _maxNumNbhdsInBatch = batchSize; var lastVariantSite = new VariantSite() { VcfReferenceAllele = "", VcfAlternateAllele = "", ReferenceName = "", VcfReferencePosition = 0 }; }
public VcfMerger(IVcfVariantSource originalVariantSource) { _variantSource = originalVariantSource; }