示例#1
0
        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);
        }
示例#2
0
        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);
        }