// ReSharper disable once UnusedMember.Global
public static long GetOffset(this Index index, string chromosomeName, int begin)
{
var refSeq = index.GetTabixReferenceSequence(chromosomeName);
if (refSeq == null)
{
return(-1);
}
// N.B. tabix assumes begin is 0-based and end is 1-based
int end = begin;
begin = AdjustBegin(begin);
if (begin == 0)
{
return(refSeq.LinearFileOffsets.FirstNonZeroValue());
}
ulong minOffset = GetMinOffset(refSeq, begin);
ulong maxOffset = GetMaxOffset(refSeq, end);
int bin = BinUtilities.ConvertPositionToBin(begin);
if (refSeq.IdToChunks.TryGetValue(bin, out Interval[] chunks))
public static long GetOffset(this Index index, string chromosomeName, int begin)
{
var refSeq = index.GetTabixReferenceSequence(chromosomeName);
if (refSeq == null)
{
return(-1);
}
// N.B. tabix assumes begin is 0-based and end is 1-based
int end = begin;
begin = AdjustBegin(begin);
if (begin == 0)
{
return(refSeq.LinearFileOffsets.FirstNonZeroValue());
}
ulong minOffset = GetMinOffset(refSeq, begin);
ulong maxOffset = GetMaxOffset(refSeq, end);
int bin = BinUtilities.ConvertPositionToBin(begin);
if (refSeq.IdToChunks.TryGetValue(bin, out var chunks))
{
return(GetMinOverlapOffset(chunks, minOffset, maxOffset));
}
int linearIndex = begin >> Constants.MinShift;
if (linearIndex >= refSeq.LinearFileOffsets.Length)
{
return(-1);
}
return((long)refSeq.LinearFileOffsets[linearIndex]);
}
public void ConvertPositionToBin_Nominal()
{
int observedResults = BinUtilities.ConvertPositionToBin(26699126);
Assert.Equal(6310, observedResults);
}
