public void GetItems_test()
{
var sequence = new SimpleSequence(new string('T', VariantUtils.MaxUpstreamLength) + "G" + new string('T', 13289 - 13284) + "C" + new string('T', 13313 - 13289) + "T", 13284 - 1 - VariantUtils.MaxUpstreamLength);
var seqProvider = new SimpleSequenceProvider(GenomeAssembly.GRCh37, sequence, ChromosomeUtilities.RefNameToChromosome);
var reader = new AncestralAlleleReader(new StreamReader(GetAncestralAlleleStream()), seqProvider);
var items = reader.GetItems().ToList();
Assert.Equal(3, items.Count);
Assert.Equal("\"g\"", items[0].GetJsonString());
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}_ancestralAlleles".Replace(' ', '_');
using (var ancestralAlleleReader = new AncestralAlleleReader(GZipUtilities.GetAppropriateStreamReader(_inputFile), 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 writer = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.AncestralAlleleTag, true, false, SaCommon.SchemaVersion, true))
{
writer.Write(ancestralAlleleReader.GetItems());
}
return(ExitCodes.Success);
}
