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($"Schema version mismatch!! Expected {SaCommon.SchemaVersion}, observed {schemaVersion} for {JsonKey}");
}
int count = memReader.ReadOptInt32();
var suppIntervals = new Dictionary <ushort, List <Interval <string> > >();
for (var i = 0; i < count; i++)
{
var saInterval = new SuppInterval(memReader);
if (suppIntervals.TryGetValue(saInterval.Chromosome.Index, out var intervals))
{
intervals.Add(new Interval <string>(saInterval.Start, saInterval.End, saInterval.GetJsonString()));
}
else
{
suppIntervals[saInterval.Chromosome.Index] = new List <Interval <string> > {
new Interval <string>(saInterval.Start, saInterval.End, saInterval.GetJsonString())
}
};
}
_intervalArrays = new Dictionary <ushort, IntervalArray <string> >(suppIntervals.Count);
foreach ((ushort chromIndex, List <Interval <string> > intervals) in suppIntervals)
{
_intervalArrays[chromIndex] = new IntervalArray <string>(intervals.ToArray());
}
}
}
public static NsiReader Read(Stream stream)
{
(IDataSourceVersion version, GenomeAssembly assembly, string jsonKey, ReportFor reportFor, int schemaVersion) = ReadHeader(stream);
if (schemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"Schema version mismatch!! Expected {SaCommon.SchemaVersion}, observed {schemaVersion} for {jsonKey}");
}
using (var blockStream = new BlockStream(new Zstandard(), stream, CompressionMode.Decompress))
using (var reader = new ExtendedBinaryReader(blockStream))
{
int count = reader.ReadOptInt32();
var suppIntervals = new Dictionary <ushort, List <Interval <string> > >();
for (var i = 0; i < count; i++)
{
var saInterval = SuppInterval.Read(reader);
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())
}
};
}
var maxChromIndex = suppIntervals.Keys.Max();
var intervalArrays = new IntervalArray <string> [maxChromIndex + 1];
for (ushort i = 0; i < intervalArrays.Length; i++)
{
intervalArrays[i] = suppIntervals.ContainsKey(i)
? new IntervalArray <string>(suppIntervals[i].ToArray())
: null;
}
return(new NsiReader(assembly, version, jsonKey, reportFor, intervalArrays));
}
}