public void TestDbSnpReader()
{
using (var dgvReader = new DgvReader(GZipUtilities.GetAppropriateStreamReader(TestDgvFile), ChromosomeUtilities.RefNameToChromosome))
{
Assert.True(dgvReader.GetItems().SequenceEqual(CreateTruthDgvItemSequence()));
}
}
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 dgvReader = new DgvReader(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.DgvTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(dgvReader.GetItems());
}
return(ExitCodes.Success);
}
