private void CreateSvTsv(string sourceName, string fileName) { if (string.IsNullOrEmpty(fileName)) { return; } var benchMark = new Benchmark(); //Console.WriteLine($"Creating TSV from {fileName}"); var dataSource = ""; var version = DataSourceVersionReader.GetSourceVersion(fileName); switch (sourceName) { case InterimSaCommon.DgvTag: dataSource = "DGV"; using (var writer = new IntervalTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.DgvSchemaVersion, InterimSaCommon.DgvTag, ReportFor.StructuralVariants)) { var reader = new DgvReader(new FileInfo(fileName), _refNamesDictionary); CreateSvTsv(reader.GetDgvItems(), writer); } break; case InterimSaCommon.ClinGenTag: dataSource = "ClinGen"; using (var writer = new IntervalTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.ClinGenSchemaVersion, InterimSaCommon.ClinGenTag, ReportFor.StructuralVariants)) { var reader = new ClinGenReader(new FileInfo(fileName), _refNamesDictionary); CreateSvTsv(reader.GetClinGenItems(), writer); } break; case InterimSaCommon.OnekSvTag: dataSource = "OnekSv"; using (var writer = new IntervalTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.OnekSvTag, ReportFor.StructuralVariants)) { var reader = new OneKGenSvReader(new FileInfo(fileName), _refNamesDictionary); CreateSvTsv(reader.GetOneKGenSvItems(), writer); } break; default: Console.WriteLine("invalid source name"); break; } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo(dataSource, version.Version, timeSpan); }
public void TestDbSnpReader() { var dgvReader = new DgvReader(TestDgvFile, RefChromDict); Assert.True(dgvReader.GetDgvItems().SequenceEqual(CreateTruthDgvItemSequence())); }