public void SingleVariantPreLoad(IPosition position)
{
var chromToPositions = new Dictionary <IChromosome, List <int> >();
PreLoadUtilities.UpdateChromToPositions(chromToPositions, position.Chromosome, position.Start, position.RefAllele, position.VcfFields[VcfCommon.AltIndex], SequenceProvider.Sequence);
_variantPositions = chromToPositions.ToImmutableDictionary();
PreLoad(position.Chromosome);
}
public void GetVariantPositions(Stream vcfStream, GenomicRange genomicRange)
{
if (vcfStream == null)
{
_variantPositions = null;
return;
}
vcfStream.Position = Tabix.VirtualPosition.From(InputStartVirtualPosition).BlockOffset;
_variantPositions = PreLoadUtilities.GetPositions(vcfStream, genomicRange, SequenceProvider).ToImmutableDictionary();
}
public void GetVariantPositions(Stream vcfStream, GenomicRange genomicRange)
{
if (vcfStream == null)
{
_variantPositions = null;
return;
}
vcfStream.Position = Tabix.VirtualPosition.From(InputStartVirtualPosition).BlockOffset;
int numPositions;
Metrics.SaPositionScan.Start();
(_variantPositions, numPositions) = PreLoadUtilities.GetPositions(vcfStream, genomicRange, SequenceProvider, RefMinorProvider);
Metrics.ShowSaPositionScanLoad(numPositions);
}