private static IntervalArray <T>[] ReadIntervals <T>(IBufferedBinaryReader reader, Func <T> readMethod) where T : IInterval
{
var numRefSeqs = reader.ReadOptInt32();
var intervalArrays = new IntervalArray <T> [numRefSeqs];
for (int refSeqIndex = 0; refSeqIndex < numRefSeqs; refSeqIndex++)
{
var numItems = reader.ReadOptInt32();
if (numItems == 0)
{
continue;
}
var intervals = new Interval <T> [numItems];
for (int i = 0; i < numItems; i++)
{
var item = readMethod();
intervals[i] = new Interval <T>(item.Start, item.End, item);
}
intervalArrays[refSeqIndex] = new IntervalArray <T>(intervals);
}
CheckGuard(reader);
return(intervalArrays);
}
public static IInterval Read(IBufferedBinaryReader reader)
{
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
return(new Interval(start, end));
}
public static CompactId Read(IBufferedBinaryReader reader)
{
var id = (IdType)reader.ReadByte();
var version = reader.ReadByte();
var info = reader.ReadUInt32();
return(new CompactId(id, version, info));
}
/// <summary>
/// check if the section guard is in place
/// </summary>
internal static void CheckGuard(IBufferedBinaryReader reader)
{
uint observedGuard = reader.ReadUInt32();
if (observedGuard != CacheConstants.GuardInt)
{
throw new InvalidDataException($"Expected a guard integer ({CacheConstants.GuardInt}), but found another value: ({observedGuard})");
}
}
public static IRegulatoryRegion Read(IBufferedBinaryReader reader, IDictionary <ushort, IChromosome> chromosomeIndexDictionary)
{
var refIndex = reader.ReadOptUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
var type = (RegulatoryRegionType)reader.ReadByte();
var id = CompactId.Read(reader);
return(new RegulatoryRegion(chromosomeIndexDictionary[refIndex], start, end, id, type));
}
internal static T[] ReadItems <T>(IBufferedBinaryReader reader, Func <T> readMethod)
{
var numItems = reader.ReadOptInt32();
var items = new T[numItems];
for (int i = 0; i < numItems; i++)
{
items[i] = readMethod();
}
CheckGuard(reader);
return(items);
}
public static IGene Read(IBufferedBinaryReader reader, IDictionary <ushort, IChromosome> indexToChromosome)
{
ushort referenceIndex = reader.ReadOptUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
bool onReverseStrand = reader.ReadBoolean();
string symbol = reader.ReadAsciiString();
int hgncId = reader.ReadOptInt32();
var entrezId = CompactId.Read(reader);
var ensemblId = CompactId.Read(reader);
return(new Gene(indexToChromosome[referenceIndex], start, end, onReverseStrand, symbol, hgncId, entrezId, ensemblId));
}
private static T[] ReadIndices <T>(IBufferedBinaryReader reader, T[] cachedItems)
{
int numItems = reader.ReadOptInt32();
var items = new T[numItems];
for (int i = 0; i < numItems; i++)
{
var index = reader.ReadOptInt32();
items[i] = cachedItems[index];
}
return(items);
}
