public TranscriptCacheReader(Stream stream)
{
var blockStream = new BlockStream(new Zstandard(), stream, CompressionMode.Decompress);
_reader = new ExtendedBinaryReader(blockStream, Encoding.UTF8);
Header = blockStream.ReadHeader(CacheHeader.Read, TranscriptCacheCustomHeader.Read) as CacheHeader;
}
private static CacheHeader GetHeader(BlockStream blockStream, out DemoCustomHeader customHeader)
{
var header = (CacheHeader)blockStream.ReadHeader(CacheHeader.Read, DemoCustomHeader.Read);
customHeader = header.CustomHeader as DemoCustomHeader;
return(header);
}
private static FileHeader GetHeader(BlockStream blockStream, out DemoCustomHeader customHeader)
{
var headerType = FileHeader.GetHeader(0, GenomeAssembly.Unknown, new DemoCustomHeader(new BlockStream.BlockPosition()));
var header = (FileHeader)blockStream.ReadHeader(headerType);
customHeader = header.Custom as DemoCustomHeader;
return(header);
}
/// <summary>
/// constructor
/// </summary>
public PredictionCacheReader(Stream fs)
{
_blockStream = new BlockStream(new Zstandard(), fs, CompressionMode.Decompress);
_reader = new BinaryReader(_blockStream, Encoding.UTF8, true);
// read the header
var headerType = PredictionCacheHeader.GetHeader(0, GenomeAssembly.Unknown, 0);
FileHeader = (PredictionCacheHeader)_blockStream.ReadHeader(headerType);
// read the LUT
_lut = ReadLookupTable(_reader);
}
private static (ushort Schema, ushort Data, ushort Vep) GetHeaderInformation(string cachePath)
{
CacheHeader header;
TranscriptCacheCustomHeader customHeader = null;
using (var stream = FileUtilities.GetReadStream(cachePath))
using (var blockStream = new BlockStream(new Zstandard(), stream, CompressionMode.Decompress))
{
header = blockStream.ReadHeader(CacheHeader.Read, TranscriptCacheCustomHeader.Read) as CacheHeader;
if (header != null)
{
customHeader = header.CustomHeader as TranscriptCacheCustomHeader;
}
}
if (header == null || customHeader == null)
{
throw new InvalidFileFormatException($"Could not parse the header information correctly for {cachePath}");
}
return(header.SchemaVersion, header.DataVersion, customHeader.VepVersion);
}
private static FileHeader GetHeader(BlockStream blockStream)
{
var headerType = FileHeader.GetHeader(0, GenomeAssembly.Unknown, new GlobalCustomHeader(0, 0));
return((FileHeader)blockStream.ReadHeader(headerType));
}
