public void AnnotationSourceConstructor()
{
var saPath = Resources.TopPath("DirectoryIntegrity");
var cacheStub = Resources.CacheGRCh37("ENST00000579787_chr1_Ensembl84");
var customAnnoPath = Resources.TopPath("DirectoryIntegrity");
var customIntervalsPath = Resources.TopPath("DirectoryIntegrity");
var conservationScoreReader = new PhylopReader(saPath);
var transcriptStream = ResourceUtilities.GetReadStream(cacheStub + ".ndb");
var siftStream = ResourceUtilities.GetReadStream(cacheStub + ".sift");
var polyPhenStream = ResourceUtilities.GetReadStream(cacheStub + ".polyphen");
var referenceStream = ResourceUtilities.GetReadStream(cacheStub + ".bases");
var streams = new AnnotationSourceStreams(transcriptStream, siftStream, polyPhenStream, referenceStream);
var customAnnotationProvider = new CustomAnnotationProvider(new[] { customAnnoPath });
var customIntervalProvider = new CustomIntervalProvider(new[] { customIntervalsPath });
var saProvider = new SupplementaryAnnotationProvider(saPath);
var annotationSource = new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader,
customAnnotationProvider, customIntervalProvider, null);
Assert.NotNull(annotationSource);
}
/// <summary>
/// constructor
/// </summary>
public UnifiedJsonWriter(StreamWriter writer, string creationTime, string vepDataVersion, IEnumerable <IDataSourceVersion> iDataSourceVersions, string genomeAssembly, string[] sampleNames)
{
_writer = writer;
_writer.NewLine = "\n";
var dataSourceVersions = iDataSourceVersions?.Select(iDataSourceVersion => iDataSourceVersion as DataSourceVersion).ToList();
// write the header
_writer.Write(UnifiedJson.GetHeader(NirvanaAnnotationSource.GetVersion(), creationTime, genomeAssembly,
JsonCommon.SchemaVersion, vepDataVersion, dataSourceVersions, sampleNames));
}
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);
}
