コード例 #1
0
        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);
        }
コード例 #2
0
        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);
        }