private static ExitCodes ProgramExecution()
{
var rootDirectory = new FileInfo(MitoMapFileNames[0]).Directory;
if (rootDirectory == null)
{
return(ExitCodes.PathNotFound);
}
var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapVar"));
var sequenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var chrom = sequenceProvider.RefNameToChromosome["chrM"];
sequenceProvider.LoadChromosome(chrom);
MitoMapInputDb mitoMapInputDb = MitoMapDatabaseUtilities.Create(_mitoMapDatabase);
var mitoMapVarReaders = MitoMapFileNames.Select(mitoMapFileName => new MitoMapVariantReader(new FileInfo(mitoMapFileName), mitoMapInputDb, sequenceProvider)).ToList();
var mergedMitoMapVarItems = MitoMapVariantReader.GetMergeAndSortedItems(mitoMapVarReaders);
string outFileName = $"{version.Name}_{version.Version}";
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, sequenceProvider, SaCommon.MitoMapTag, false, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(mergedMitoMapVarItems);
}
return(ExitCodes.Success);
}
public static List <string> GetPubMedIds(string field, MitoMapInputDb mitoMapInputDb)
{
if (field == "0")
{
return(default);