internal static ulong GetMinOffset(ReferenceSequence refSeq, int begin)
{
int bin = BinUtilities.FirstBin(Constants.NumLevels) + (begin >> Constants.MinShift);
do
{
if (refSeq.IdToChunks.ContainsKey(bin))
{
break;
}
int firstBin = (BinUtilities.ParentBin(bin) << 3) + 1;
if (bin > firstBin)
{
bin--;
}
else
{
bin = BinUtilities.ParentBin(bin);
}
} while (bin != 0);
int bottomBin = BinUtilities.BottomBin(bin);
return(refSeq.LinearFileOffsets[bottomBin]);
}
// 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))
protected override void WriteContent(BinaryWriter bw)
{
bw.Write((byte)BinUtilities.PackType(this.ValueType));
bw.Write(this.Value is not null);
if (this.Value is not null)
{
this.Value.Write(bw, false);
}
}
internal BinTreeOptional(BinaryReader br, IBinTreeParent parent, uint nameHash) : base(parent, nameHash)
{
this.ValueType = BinUtilities.UnpackType((BinPropertyType)br.ReadByte());
bool isSome = br.ReadBoolean();
if (isSome)
{
this.Value = BinTreeProperty.Read(br, this, this.ValueType);
}
}
private string GetPropertyTypeDeclaration(MetaDumpProperty property, Dictionary <uint, string> classNames)
{
return(BinUtilities.UnpackType(property.Type) switch
{
BinPropertyType.Container => GetContainerTypeDeclaration(property.OtherClass, property.Container, false, classNames),
BinPropertyType.UnorderedContainer => GetContainerTypeDeclaration(property.OtherClass, property.Container, true, classNames),
BinPropertyType.Structure => GetStructureTypeDeclaration(property.OtherClass, classNames),
BinPropertyType.Embedded => GetEmbeddedTypeDeclaration(property.OtherClass, classNames),
BinPropertyType.Optional => GetOptionalTypeDeclaration(property.OtherClass, property.Container, classNames),
BinPropertyType.Map => GetMapTypeDeclaration(property.OtherClass, property.Map, classNames),
BinPropertyType type => GetPrimitivePropertyTypeDeclaration(type, true)
});
private void WritePropertyAttribute(StreamWriter sw, MetaDumpProperty property, Dictionary <uint, string> propertyNames)
{
BinPropertyType propertyType = BinUtilities.UnpackType(property.Type);
if (propertyNames.TryGetValue(property.Hash, out string propertyName))
{
sw.WriteLineIndented(2, @"[MetaProperty(""{0}"", BinPropertyType.{1})]", propertyName, propertyType);
}
else
{
sw.WriteLineIndented(2, @"[MetaProperty({0}, BinPropertyType.{1})]", property.Hash, propertyType);
}
}
public void OverlappingBinsWithVariants_EndBeyondMaxRefLen_CorrectEnd()
{
const int expectedBinId = 6310;
var idToChunks = new Dictionary <int, Interval[]>
{
[expectedBinId] = new[] { new Interval(1, 1) }
};
List <int> results = BinUtilities.OverlappingBinsWithVariants(10, int.MaxValue, idToChunks).ToList();
Assert.Single(results);
Assert.Equal(expectedBinId, results[0]);
}
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]);
}
internal static ulong GetMaxOffset(ReferenceSequence refSeq, int end)
{
int bin = BinUtilities.FirstBin(Constants.NumLevels) + ((end - 1) >> Constants.MinShift) + 1;
while (true)
{
while (bin % 8 == 1)
{
bin = BinUtilities.ParentBin(bin);
}
if (bin == 0)
{
return(ulong.MaxValue);
}
if (refSeq.IdToChunks.TryGetValue(bin, out var chunks) && chunks.Length > 0)
{
return(chunks[0].Begin);
}
bin++;
}
}
public void BottomBin_Nominal()
{
int observedResults = BinUtilities.BottomBin(12517);
Assert.Equal(7836, observedResults);
}
public void ConvertPositionToBin_Nominal()
{
int observedResults = BinUtilities.ConvertPositionToBin(26699126);
Assert.Equal(6310, observedResults);
}
public void OverlappingBinsWithVariants_EndBeforeBegin_ReturnEmptyList()
{
IEnumerable <int> results = BinUtilities.OverlappingBinsWithVariants(20, 10, null);
Assert.Empty(results);
}
