public void Write(Dictionary <string, List <ISuppGeneItem> > geneToEntries)
{
using (var memStream = new MemoryStream())
using (var memWriter = new ExtendedBinaryWriter(memStream))
using (var writer = new BinaryWriter(_nsaStream))
{
_version.Write(memWriter);
memWriter.WriteOptAscii(_jsonKey);
memWriter.Write(_isArray);
memWriter.WriteOpt(_schemaVersion);
memWriter.WriteOpt(geneToEntries.Count);
foreach ((string geneSymbol, var entries) in geneToEntries)
{
memWriter.WriteOptAscii(geneSymbol);
memWriter.WriteOpt(entries.Count);
foreach (ISuppGeneItem geneItem in entries)
{
memWriter.Write(geneItem.GetJsonString());
}
}
var uncompressedBytes = memStream.ToArray();
var compressedBytes = new byte[uncompressedBytes.Length + 32];
var compressor = new Zstandard();
var compressSize = compressor.Compress(uncompressedBytes, uncompressedBytes.Length, compressedBytes,
compressedBytes.Length);
writer.Write(compressedBytes, 0, compressSize);
Console.WriteLine("Number of gene entries written:" + geneToEntries.Count);
}
}
public int Write(IEnumerable <ISuppIntervalItem> siItems)
{
var sortedItems = siItems.OrderBy(x => x.Chromosome.Index).ThenBy(x => x.Start).ThenBy(x => x.End).ToList();
Console.WriteLine($"Writing {sortedItems.Count} intervals to database...");
_memWriter.WriteOpt(sortedItems.Count);
foreach (ISuppIntervalItem item in sortedItems)
{
_memWriter.WriteOptAscii(item.Chromosome.EnsemblName);
_memWriter.WriteOptAscii(item.Chromosome.UcscName);
_memWriter.WriteOpt(item.Chromosome.Index);
_memWriter.WriteOpt(item.Start);
_memWriter.WriteOpt(item.End);
_memWriter.Write(item.GetJsonString());
}
var uncompressedBytes = _memStream.ToArray();
var compressedBytes = new byte[uncompressedBytes.Length + 32];
var compressor = new Zstandard();
var compressSize = compressor.Compress(uncompressedBytes, uncompressedBytes.Length, compressedBytes,
compressedBytes.Length);
_writer.Write(compressedBytes, 0, compressSize);
_writer.Flush();
return(sortedItems.Count);
}
private void WriteCompressed(int lastPosition)
{
var startLocation = _writer.BaseStream.Position;
int compressSize = _zstd.Compress(_scores, lastPosition, _compressedScores, _compressedScores.Length);
_writer.Write(_compressedScores, 0, compressSize);
_index.Add(_chromIndex, startLocation, compressSize);
Array.Clear(_scores, 0, _scores.Length);
_memStream.Position = 0;//reset the stream
}
