/// <summary>
/// constructor
/// </summary>
public MockSupplementaryAnnotationProvider(ISupplementaryAnnotationReader saReader, ChromosomeRenamer renamer)
{
if (saReader == null)
{
return;
}
_saReader = saReader;
_overlappingSupplementaryIntervals = new List <ISupplementaryInterval>();
_suppIntervalForest = _saReader.GetIntervalForest(renamer);
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
if (string.IsNullOrEmpty(_saDir) || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
var saPath = Path.Combine(_saDir, ucscReferenceName + ".nsa");
_saReader = File.Exists(saPath) ? new SupplementaryAnnotationReader(saPath) : null;
_intervalForest = _saReader?.GetIntervalForest(renamer);
_hasIntervals = !(_intervalForest is NullIntervalSearch <ISupplementaryInterval>);
_currentUcscReferenceName = ucscReferenceName;
}
