private static ExitCodes ProgramExecution()
{
using var mitoHeteroplasmyParser = new MitoHeteroplasmyParser(GZipUtilities.GetAppropriateReadStream(_inputFile));
using var tsvStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, OutFileName));
using var tsvWriter = new StreamWriter(tsvStream);
tsvWriter.WriteLine(HeaderLine);
foreach (var line in mitoHeteroplasmyParser.GetOutputLines())
{
tsvWriter.WriteLine(line);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var primateAiParser = new MitoHeteroplasmyParser(GZipUtilities.GetAppropriateReadStream(_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 nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.MitoHeteroplasmyTag, true, false, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(primateAiParser.GetItems());
}
return(ExitCodes.Success);
}