internal static IAnnotatedVariant GetVariant(string cachePath, ISupplementaryAnnotationReader saReader,
string vcfLine, IConservationScoreReader csReader)
{
var annotationSource = ResourceUtilities.GetAnnotationSource(cachePath, saReader, csReader);
return(GetVariant(annotationSource, vcfLine));
}
/// <summary>
/// creates a new annotation source with data from the micro-cache file
/// </summary>
internal static IAnnotationSource GetAnnotationSource(string cachePath, ISupplementaryAnnotationReader saReader,
IConservationScoreReader conservationScoreReader = null,
ISupplementaryAnnotationProvider customAnnotationProvider = null,
ISupplementaryAnnotationProvider customIntervalProvider = null)
{
var streams = GetAnnotationSourceStreams(cachePath);
var renamer = ChromosomeRenamer.GetChromosomeRenamer(GetReadStream($"{cachePath}.bases"));
var saProvider = new MockSupplementaryAnnotationProvider(saReader, renamer);
PerformanceMetrics.DisableOutput = true;
return(new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader, customAnnotationProvider,
customIntervalProvider, null));
}
