// constructor
public SupplementaryAnnotationReader(Stream dbStream, Stream idxStream, string saPath = null)
{
// open the database file
_stream = dbStream;
_idxStream = idxStream;
_reader = new ExtendedBinaryReader(_stream);
_index = new SaIndex(new ExtendedBinaryReader(idxStream));
// check the header
Header = GetHeader(_reader, out _intervalsPosition, saPath);
}
// constructor
public SupplementaryAnnotationWriter(string saPath, string currentRefSeq, List <DataSourceVersion> dataSourceVersions, GenomeAssembly genomeAssembly = GenomeAssembly.Unknown)
{
_dataSourceVersions = dataSourceVersions;
_saPath = saPath;
_currentRefSeq = currentRefSeq;
_currentGenomeAssembly = genomeAssembly;
_stream = FileUtilities.GetCreateStream(saPath);
_writer = new ExtendedBinaryWriter(_stream);
_index = new SaIndex();
WriteHeader();
}
/// <summary>
/// protected implementation of Dispose pattern.
/// </summary>
private void Dispose(bool disposing)
{
if (disposing)
{
_stream.Dispose();
_idxStream.Dispose();
}
_reader = null;
_stream = null;
_idxStream = null;
_index = null;
}
/// <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;
}
