public NsaReader(Stream dataStream, Stream indexStream, int blockSize = SaCommon.DefaultBlockSize)
{
_stream = dataStream;
_blockSize = blockSize;
_reader = new ExtendedBinaryReader(_stream);
_block = new NsaBlock(new Zstandard(), blockSize);
_index = new NsaIndex(indexStream);
Assembly = _index.Assembly;
Version = _index.Version;
JsonKey = _index.JsonKey;
MatchByAllele = _index.MatchByAllele;
IsArray = _index.IsArray;
IsPositional = _index.IsPositional;
if (_index.SchemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"SA schema version mismatch. Expected {SaCommon.SchemaVersion}, observed {_index.SchemaVersion} for {JsonKey}");
}
_annotations = new List <AnnotationItem>(64 * 1024);
_annotationBuffer = new byte[1024 * 1024];
_annotationStream = new MemoryStream(_annotationBuffer);
_annotationReader = new ExtendedBinaryReader(_annotationStream);
}
public IEnumerable <NsaBlock> GetCompressedBlocks(ushort chromIndex)
{
var(location, blockCount) = _index.GetFileRange(chromIndex, 1, int.MaxValue);
if (location == -1)
{
yield break;
}
_reader.BaseStream.Position = location;
for (var i = 0; i < blockCount; i++)
{
var block = new NsaBlock(new Zstandard(), _blockSize);
block.ReadCompressedBytes(_reader);
yield return(block);
}
}
