private void CloseCurrentSaWriter()
{
if (_currentRefName == null)
{
return;
}
//write last SA item
if (!_prevSaCreator.IsEmpty())
{
_saWriter.Write(_prevSaCreator, _prevSaCreator.ReferencePosition);
_numSaWritten++;
}
// reset _prevSa
_prevSaCreator = null;
// write the intervals
_saWriter.SetIntervalList(_supplementaryIntervalList);
Console.WriteLine("No of intervals: {0}", _supplementaryIntervalList.Count);
_saWriter.Dispose();
double lookupsPerSecond;
Console.WriteLine("No of annotations : {0}", _numSaWritten);
Console.WriteLine("{0} supplementary annotations written - {1}", _numSaWritten,
_creationBench.GetElapsedIterationTime(_numSaWritten, "variants", out lookupsPerSecond));
Console.WriteLine("No of ref minor positions: {0}", _saWriter.RefMinorCount);
}
/// <summary>
/// writes the annotations to the current database file
/// </summary>
public void Write(SupplementaryPositionCreator spCreator, int referencePos, bool finalizePositinalAnnotation = true)
{
if (finalizePositinalAnnotation)
{
spCreator.FinalizePositionalAnnotations();
}
if (spCreator.IsEmpty())
{
return;
}
// add this entry to the index
var currentOffset = _stream.Position;
_index.Add((uint)referencePos, (uint)currentOffset, spCreator.IsRefMinor());
if (spCreator.IsRefMinor())
{
RefMinorCount++;
}
spCreator.WriteAnnotation(_writer);
}
public void CreateDatabase()
{
var unsorted = 0;
_creationBench = new Benchmark();
_prevSaCreator = null;
// loading ref sequence
var saCreator = GetNextSupplementaryAnnotation();
while (saCreator != null)
{
if (!_currentRefName.Equals(saCreator.RefSeqName)) //sanity check
{
throw new Exception("Error: currentRef != sa ref");
}
if (_saWriter == null) //check for empty writer
{
Console.WriteLine("Supplementary annotationa writer was not initialized");
return;
}
// this SA is not the first one in current contig
if (_prevSaCreator != null)
{
if (saCreator.ReferencePosition == _prevSaCreator.ReferencePosition)
{
_prevSaCreator.MergeSaCreator(saCreator);
}
else
{
if (_prevSaCreator.RefSeqName == saCreator.RefSeqName && _prevSaCreator.ReferencePosition > saCreator.ReferencePosition)
{
Console.WriteLine("Unsorted records:{0}, {1}, {2}, {3}", _prevSaCreator.RefSeqName,
_prevSaCreator.ReferencePosition, saCreator.RefSeqName, saCreator.ReferencePosition);
unsorted++;
}
if (!_prevSaCreator.IsEmpty())
{
_saWriter.Write(_prevSaCreator, _prevSaCreator.ReferencePosition);
_numSaWritten++;
}
_prevSaCreator = saCreator;
}
}
else
{
_prevSaCreator = saCreator;
}
saCreator = GetNextSupplementaryAnnotation();
}
// do not forgot to write the last item
CloseCurrentSaWriter();
Console.WriteLine("");
Console.WriteLine("unsorted records: {0}", unsorted);
}