public ParallelSaTsvReader(string fileName) { _fileName = fileName; using (var tsvIndex = new TsvIndex(new BinaryReader(FileUtilities.GetReadStream(_fileName + TsvIndex.FileExtension)))) { _refNameOffsets = tsvIndex.TagPositions; } }
public IntervalTsvWriter(string outputPath, DataSourceVersion dataSourceVersion, string assembly, int dataVersion, string keyName, ReportFor reportingFor) { var fileName = keyName + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".interval.tsv.gz"; _bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputPath, fileName)); _bgzipTextWriter.Write(GetHeader(dataSourceVersion, dataVersion, assembly, keyName, reportingFor)); _tsvIndex = new TsvIndex(Path.Combine(outputPath, fileName) + ".tvi"); }
public SaMiscTsvWriter(string outputPath, DataSourceVersion dataSourceVersion, string assembly, string keyName, ISequenceProvider sequenceProvider) { var fileName = keyName + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".misc.tsv.gz"; _bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputPath, fileName)); _bgzipTextWriter.Write(GetHeader(dataSourceVersion, assembly)); _tsvIndex = new TsvIndex(Path.Combine(outputPath, fileName + ".tvi")); _sequenceProvider = sequenceProvider; }
private SaTsvWriter(string outputDir, DataSourceVersion dataSourceVersion, string assembly, int schemaVersion, string jsonKey, string vcfKeys, bool isAlleleSpecific, bool isArray = false) { var fileName = jsonKey + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".tsv.gz"; _bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputDir, fileName)); _bgzipTextWriter.Write(GetHeader(dataSourceVersion, schemaVersion, assembly, jsonKey, vcfKeys, isAlleleSpecific, isArray)); _tsvIndex = new TsvIndex(Path.Combine(outputDir, fileName + ".tvi")); }