// ReSharper disable once UnusedMember.Global
public bool HasVariants(string chromosomeName, int begin, int end)
{
var refSeq = _index.GetTabixReferenceSequence(chromosomeName);
if (refSeq == null)
{
return(false);
}
int adjBegin = SearchUtilities.AdjustBegin(begin);
IEnumerable <int> bins = BinUtilities.OverlappingBinsWithVariants(adjBegin, end, refSeq.IdToChunks);
var block = new BgzfBlock();
foreach (int bin in bins)
{
refSeq.IdToChunks.TryGetValue(bin, out Interval[] chunks);
if (HasVariantsInBin(refSeq.Chromosome, begin, end, block, chunks))
{
return(true);
}
}
return(false);
}
public bool HasVariants(string chromosomeName, int begin, int end)
{
var refSeq = _index.GetTabixReferenceSequence(chromosomeName);
if (refSeq == null)
{
return(false);
}
int adjBegin = SearchUtilities.AdjustBegin(begin);
int beginBin = BinUtilities.ConvertPositionToBin(adjBegin);
int endBin = BinUtilities.ConvertPositionToBin(end);
int binDiff = endBin - beginBin;
// we can use the tabix index to investigate if any of the internal bins have variants
if (binDiff >= 2)
{
bool hasInternalVariants = HasVariantsInAnyBins(refSeq.IdToChunks, beginBin + 1, endBin - 1);
if (hasInternalVariants)
{
return(true);
}
}
// finally we have to check the remaining (edge) bins
var block = new BgzfBlock();
refSeq.IdToChunks.TryGetValue(beginBin, out var beginChunks);
refSeq.IdToChunks.TryGetValue(endBin, out var endChunks);
return(HasVariantsInBin(refSeq.Chromosome, begin, end, block, beginChunks) ||
HasVariantsInBin(refSeq.Chromosome, begin, end, block, endChunks));
}
private bool HasVariantsInBin(IChromosome chromosome, int begin, int end, BgzfBlock block, Interval[] intervals)
{
(long minVirtualOffset, long maxVirtualOffset) = SearchUtilities.GetMinMaxVirtualFileOffset(intervals);
long minOffset = VirtualPosition.From(minVirtualOffset).FileOffset;
long maxOffset = VirtualPosition.From(maxVirtualOffset).FileOffset;
return(BgzfBlockVcfReader.FindVariantsInBlocks(_vcfStream, minOffset, maxOffset, block, chromosome, begin, end));
}
public static bool FindVariantsInBlocks(Stream stream, long beginOffset, long endOffset, BgzfBlock block,
IChromosome chromosome, int start, int end)
{
stream.Position = beginOffset;
while (stream.Position <= endOffset)
{
string blockString = block.Read(stream);
if (HasVcfPositionsOnInterval(blockString, chromosome, start, end))
{
return(true);
}
}
return(false);
}