public void GetItems()
{
using (var reader = new RefMinorReader(new StreamReader(GetStream()), GetSequenceProvider()))
{
var items = reader.GetItems().ToList();
Assert.Equal(3, items.Count);
}
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}_{SaCommon.RefMinorTag}".Replace(' ', '_');
using (var refMinorReader = new RefMinorReader(GZipUtilities.GetAppropriateStreamReader(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.RefMinorFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.RefMinorFileSuffix + SaCommon.IndexSufix)))
using (var writer = new RefMinorDbWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.SchemaVersion))
{
writer.Write(refMinorReader.GetItems());
}
return(ExitCodes.Success);
}
public void LoopBack()
{
var version = new DataSourceVersion("onekgen", "v0.3", DateTime.Now.Ticks);
using (var reader = new RefMinorReader(new StreamReader(GetStream()), GetSequenceProvider()))
using (var stream = new MemoryStream())
using (var indexStream = new MemoryStream())
using (var writer = new RefMinorDbWriter(new ExtendedBinaryWriter(stream), new ExtendedBinaryWriter(indexStream), version, GetSequenceProvider(), SaCommon.SchemaVersion))
{
writer.Write(reader.GetItems());
stream.Position = 0;
indexStream.Position = 0;
using (var dbReader = new RefMinorDbReader(stream, indexStream))
{
Assert.Equal("T", dbReader.GetGlobalMajorAllele(ChromosomeUtilities.Chr1, 15274));
Assert.Null(dbReader.GetGlobalMajorAllele(ChromosomeUtilities.Chr1, 1524));
}
}
}
