public void OneRcv_oneVcv()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 31496350, "C");
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000124712.xml")),
FileUtilities.GetReadStream(Resources.VcvXmlFiles("VCV000137106.xml")), sequenceProvider);
var items = reader.GetItems().ToArray();
Assert.Equal(2, items.Length);
}
private static ExitCodes ProgramExecution()
{
var version = DataSourceVersionReader.GetSourceVersion(_rcvFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)))
using (var clinvarReader = new ClinVarReader(GZipUtilities.GetAppropriateReadStream(_rcvFile), GZipUtilities.GetAppropriateReadStream(_vcvFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.ClinvarTag, false, true, SaCommon.SchemaVersion, false))
using (var schemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(schemaStream))
{
nsaWriter.Write(clinvarReader.GetItems());
schemaWriter.Write(clinvarReader.JsonSchema);
}
return(ExitCodes.Success);
}
