public void Readback_clingen()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
{
using (var siWriter = new NsiWriter(saStream, version, GenomeAssembly.GRCh37, "clingen",
ReportFor.StructuralVariants, SaCommon.SchemaVersion, true))
{
siWriter.Write(GetClinGenItems());
}
saStream.Position = 0;
var siReader = NsiReader.Read(saStream);
var annotations = siReader.GetAnnotation(new Variant(ChromosomeUtilities.Chr1, 100, 14590, "", "<DEL>", VariantType.deletion, "1:100:14590:del", false, false, false, null, null, true)).ToArray();
string[] expected =
{
"\"chromosome\":\"1\",\"begin\":145,\"end\":2743,\"variantType\":\"copy_number_gain\",\"id\":\"cg1\",\"clinicalInterpretation\":\"likely benign\",\"phenotypes\":[\"phenotype1\",\"phenotype2\"],\"phenotypeIds\":[\"pid1\",\"pid2\"],\"observedGains\":3,\"validated\":true,\"reciprocalOverlap\":0.17935,\"annotationOverlap\":1",
"\"chromosome\":\"1\",\"begin\":14585,\"end\":5872743,\"variantType\":\"copy_number_loss\",\"id\":\"cg2\",\"clinicalInterpretation\":\"likely pathogenic\",\"phenotypes\":[\"phenotype3\",\"phenotype5\"],\"phenotypeIds\":[\"pid3\",\"pid5\"],\"observedLosses\":5,\"validated\":true,\"reciprocalOverlap\":0,\"annotationOverlap\":0"
};
Assert.Equal(2, annotations.Length);
Assert.Equal(expected, annotations);
}
}
public static IAnnotationProvider GetNsaProvider(AnnotationFiles files)
{
if (files == null)
{
return(null);
}
//todo: use using block to release nsa streams
var nsaReaders = files.NsaFiles?.Select(x => new NsaReader(PersistentStreamUtils.GetReadStream(x.Nsa), PersistentStreamUtils.GetReadStream(x.Idx)))
.OrderBy(x => x.JsonKey, StringComparer.Ordinal).ToArray() ?? new INsaReader[] { };
//todo: use using block to release nsi streams
var nsiReaders = files.NsiFiles?.Select(x => NsiReader.Read(PersistentStreamUtils.GetReadStream(x)))
.OrderBy(x => x.JsonKey, StringComparer.Ordinal).ToArray() ?? new INsiReader[] { };
if (nsaReaders.Length == 0 && nsiReaders.Length == 0)
{
return(null);
}
return(new NsaProvider(nsaReaders, nsiReaders));
}
public LcrProvider(Stream stream)
{
_nsiReader = NsiReader.Read(stream);
Assembly = _nsiReader.Assembly;
DataSourceVersions = new[] { _nsiReader.Version };
}
