public IAnnotationSource CreateAnnotationSource(IAnnotatorInfo annotatorInfo, IAnnotatorPaths annotatorPaths)
{
var conservationScoreReader = new PhylopReader(annotatorPaths.SupplementaryAnnotation);
var transcriptStream = FileUtilities.GetReadStream(CacheConstants.TranscriptPath(annotatorPaths.CachePrefix));
var siftStream = FileUtilities.GetReadStream(CacheConstants.SiftPath(annotatorPaths.CachePrefix));
var polyPhenStream = FileUtilities.GetReadStream(CacheConstants.PolyPhenPath(annotatorPaths.CachePrefix));
var referenceStream = FileUtilities.GetReadStream(annotatorPaths.CompressedReference);
var streams = new AnnotationSourceStreams(transcriptStream, siftStream, polyPhenStream, referenceStream);
var caProvider = annotatorPaths.CustomAnnotation.Any() ? new CustomAnnotationProvider(annotatorPaths.CustomAnnotation) : null;
var ciProvider = annotatorPaths.CustomIntervals.Any() ? new CustomIntervalProvider(annotatorPaths.CustomIntervals) : null;
var saProvider = annotatorPaths.SupplementaryAnnotation != null ? new SupplementaryAnnotationProvider(annotatorPaths.SupplementaryAnnotation) : null;
//adding the saPath because OMIM needs it
var annotationSource = new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader, caProvider, ciProvider, annotatorPaths.SupplementaryAnnotation);
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.ReferenceNoCall))
{
annotationSource.EnableReferenceNoCalls(annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.TranscriptOnlyRefNoCall));
}
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.EnableMitochondrialAnnotation))
{
annotationSource.EnableMitochondrialAnnotation();
}
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.ReportAllSvOverlappingTranscripts))
{
annotationSource.EnableReportAllSvOverlappingTranscripts();
}
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.EnableLoftee))
{
annotationSource.AddPlugin(new Loftee());
}
return(annotationSource);
}
