public void GetItems()
{
using (var reader = new ClinGenReader(new StreamReader(GetStream()), ChromosomeUtilities.RefNameToChromosome))
{
var items = reader.GetItems().ToList();
Assert.Equal(4, items.Count);
Assert.Equal("\"chromosome\":\"1\",\"begin\":564405,\"end\":8597804,\"variantType\":\"copy_number_loss\",\"id\":\"nsv530705\",\"clinicalInterpretation\":\"pathogenic\",\"phenotypes\":[\"Developmental delay AND/OR other significant developmental or morphological phenotypes\"],\"observedLosses\":1", items[0].GetJsonString());
}
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFileName + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var clinGenReader = new ClinGenReader(GZipUtilities.GetAppropriateStreamReader(_inputFileName), referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsaStream), version, referenceProvider.Assembly, SaCommon.ClinGenTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(clinGenReader.GetItems());
}
return(ExitCodes.Success);
}