public NsiReader(Stream stream)
{
_stream = stream;
var compressData = new byte[MaxStreamLength];
int length = stream.Read(compressData, 0, MaxStreamLength);
//uncompress
var zstd = new Zstandard();
var decompressedLength = zstd.GetDecompressedLength(compressData, length);
var decompressedData = new byte[decompressedLength];
zstd.Decompress(compressData, length, decompressedData, decompressedLength);
using (var memStream = new MemoryStream(decompressedData, 0, decompressedLength))
using (var memReader = new ExtendedBinaryReader(memStream))
{
Version = DataSourceVersion.Read(memReader);
Assembly = (GenomeAssembly)memReader.ReadByte();
JsonKey = memReader.ReadAsciiString();
ReportFor = (ReportFor)memReader.ReadByte();
int schemaVersion = memReader.ReadOptInt32();
if (schemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"Schema version mismatch!! Expected {SaCommon.SchemaVersion}, observed {schemaVersion} for {JsonKey}");
}
int count = memReader.ReadOptInt32();
var suppIntervals = new Dictionary <ushort, List <Interval <string> > >();
for (var i = 0; i < count; i++)
{
var saInterval = new SuppInterval(memReader);
if (suppIntervals.TryGetValue(saInterval.Chromosome.Index, out var intervals))
{
intervals.Add(new Interval <string>(saInterval.Start, saInterval.End, saInterval.GetJsonString()));
}
else
{
suppIntervals[saInterval.Chromosome.Index] = new List <Interval <string> > {
new Interval <string>(saInterval.Start, saInterval.End, saInterval.GetJsonString())
}
};
}
_intervalArrays = new Dictionary <ushort, IntervalArray <string> >(suppIntervals.Count);
foreach ((ushort chromIndex, List <Interval <string> > intervals) in suppIntervals)
{
_intervalArrays[chromIndex] = new IntervalArray <string>(intervals.ToArray());
}
}
}
private void PreLoad(IChromosome chrom)
{
_chromosome = chrom;
(long startLocation, int numBytes) = _index.GetFileRange(chrom.Index);
if (startLocation == -1)
{
_lastPhylopPosition = -1;
return;
}
_reader.BaseStream.Position = startLocation;
var buffer = _reader.ReadBytes(numBytes);
_lastPhylopPosition = _zstd.Decompress(buffer, buffer.Length, _scores, _scores.Length);
}
public NgaReader(Stream stream)
{
_nsaStream = stream;
// read the whole file. Currently they are well under 2MB
var compressedBytes = new byte[2 * 1024 * 1024];
var decompressedBytes = new byte[20 * 1024 * 1024];
var compressedSize = _nsaStream.Read(compressedBytes, 0, compressedBytes.Length);
var zstd = new Zstandard();
var decompressedSize = zstd.Decompress(compressedBytes, compressedSize, decompressedBytes, decompressedBytes.Length);
_memStream = new MemoryStream(decompressedBytes, 0, decompressedSize);
_reader = new ExtendedBinaryReader(_memStream);
Version = DataSourceVersion.Read(_reader);
JsonKey = _reader.ReadAsciiString();
_isArray = _reader.ReadBoolean();
ushort schemaVersion = _reader.ReadOptUInt16();
if (schemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"Expected schema version: {SaCommon.SchemaVersion}, observed: {schemaVersion} for {JsonKey}");
}
}
