private void SendWriter(ExtendedBinaryWriter writer)
{
writer?.Flush();
var fullUri = new Uri(_uri, "diag?sid=" + _sessionId + (_contextName != null ? "&ctx=" + _contextName : ""));
var binaryContent = writer != null
? (writer.BaseStream as MemoryStream).ToArray()
: Array.Empty <byte>();
using (var content = new ByteArrayContent(binaryContent))
{
try
{
var response = _client.PostAsync(fullUri, content).Result;
var responseBody = response.Content.ReadAsStringAsync().Result;
if (responseBody != "ACK")
{
_communicationErrorCount++;
}
}
catch (Exception)
{
_communicationErrorCount++;
}
}
writer?.BaseStream.Dispose();
writer?.Dispose();
}
public void Write(string name, string bases, int seqOffset = 0)
{
_writer.Flush();
long position = _stream.Position;
_refSeqNames.Add(name);
_refSeqIndex.Add(new SequenceIndexEntry
{
NumBases = bases.Length,
FileOffset = position,
SequenceOffset = seqOffset
});
_sequenceCompressor.Compress(bases, _twoBitSequence);
// sort the masked intervals
var sortedMaskedIntervals = _twoBitSequence.MaskedIntervals.OrderBy(x => x.Begin).ThenBy(x => x.End).ToList();
_refSeqMaskedIntervals.Add(sortedMaskedIntervals);
_writer.Write(_twoBitSequence.Buffer, 0, _twoBitSequence.NumBufferBytes);
}
/// <summary>
/// protected implementation of Dispose pattern.
/// </summary>
private void Dispose(bool disposing)
{
if (disposing)
{
// write a negative length
_writer.WriteOpt(-1);
// write the intervals
WriteSupplementaryIntervals();
// write the guard integer
_writer.Flush();
_eofOffset = _stream.Position;
_writer.Write(SupplementaryAnnotationCommon.GuardInt);
// update the offsets in the header
_stream.Position = _offsetHeader;
_writer.Write(_dataSourceVersionsOffset);
_writer.Write(_dataOffset);
_writer.Write(_intervalOffset);
_writer.Write(_eofOffset);
// close the file streams
_writer.Dispose();
_stream.Dispose();
_index.Write(_saPath + ".idx", _currentRefSeq);
}
// reset all the class variables
_stream = null;
_dataSourceVersionsOffset = 0;
_dataOffset = 0;
_eofOffset = 0;
_offsetHeader = 0;
_intervalOffset = 0;
_index = null;
}
internal void Write(List <Creation.ReferenceSequence> referenceSequences)
{
_writer.Flush();
long indexOffset = _stream.Position;
int indexSize = 8 + IndexEntry.Size * referenceSequences.Count;
var buffers = new List <ReferenceBuffer>(referenceSequences.Count);
ushort refIndex = 0;
foreach (var referenceSequence in referenceSequences)
{
buffers.Add(referenceSequence.GetReferenceBuffer(refIndex));
refIndex++;
}
IndexEntry[] index = CreateIndex(buffers, indexOffset, indexSize);
WriteIndex(index);
WriteReferenceBuffers(buffers);
}
public static byte[] Compress(byte[] uncompressedData)
{
using (var outputMemoryStream = new MemoryStream())
{
using (var output = new ExtendedBinaryWriter(outputMemoryStream))
{
var pos = 0;
var chunkCount = (int)(uncompressedData.Length / (double)CHUNK_SIZE_UNC_MAX);
while (pos < uncompressedData.Length)
{
var data = CompressChunk(uncompressedData, ref pos);
output.Write((ushort)(data.Length + 2));
output.Write(data);
output.Write((byte)chunkCount);
chunkCount--;
}
output.Flush();
}
return(outputMemoryStream.ToArray());
}
}
