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
};
}
