private static IEnumerable <ISupplementaryDataItem> GetItems(IEnumerable <string> filePaths,
ISequenceProvider referenceProvider)
{
IEnumerable <ISupplementaryDataItem> items = null;
foreach (string filePath in filePaths)
{
var fileStreamReader = GZipUtilities.GetAppropriateStreamReader(filePath);
var reader = new GnomadReader(fileStreamReader, referenceProvider);
items = items == null?reader.GetItems() : items.Concat(reader.GetItems());
}
return(items);
}
private static void CreateNsa(string[] exomeFiles, string genomeFile, DataSourceVersion version)
{
Console.WriteLine($"Processing file: {genomeFile}");
var outName = Path.GetFileNameWithoutExtension(genomeFile);
using (var exomeReader = GetExomeReader(exomeFiles, genomeFile))
using (var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_tempDirectory, outName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_tempDirectory, outName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.GnomadTag, true, false, SaCommon.SchemaVersion, false))
using (var reader = GZipUtilities.GetAppropriateStreamReader(genomeFile))
{
var gnomadReader = new GnomadReader(reader, exomeReader, referenceProvider);
var count = nsaWriter.Write(gnomadReader.GetCombinedItems());
Console.WriteLine($"Wrote {count} items to NSA file.");
}
}
