public void GetItems_test()
{
var reader = new GlobalMinorReader(GetStream(), _chromDict);
var items = reader.GetItems().Cast <ISupplementaryDataItem>().ToList();
var globalMinor = SuppDataUtilities.GetPositionalAnnotation(items);
Assert.Equal("{\"globalMinorAllele\":\"G\",\"globalMinorAlleleFrequency\":0.3472}", globalMinor.GetJsonString());
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var globalMinorReader = new GlobalMinorReader(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider.RefNameToChromosome);
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}_globalMinor";
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.GlobalAlleleTag, true, false, SaCommon.SchemaVersion, true))
{
nsaWriter.Write(globalMinorReader.GetItems());
}
return(ExitCodes.Success);
}
