/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="sorter">Sorter instance.</param> /// <param name="unsortedDeltaStream">Unsorted Delta Filename.</param> /// <param name="queryParser">Query/read sequences parser.</param> /// <param name="outputStream">Output file name.</param> public static void WriteSortedDelta(DeltaAlignmentSorter sorter, Stream unsortedDeltaStream, FastASequencePositionParser queryParser, Stream outputStream) { if (sorter == null) { throw new ArgumentNullException("sorter"); } using (DeltaAlignmentParser unsortedDeltaParser = new DeltaAlignmentParser(unsortedDeltaStream, queryParser)) { using (StreamWriter writer = new StreamWriter(outputStream)) { long deltaPositionInFile = 0; foreach (long id in sorter.GetSortedIds()) { DeltaAlignment deltaAlignment = unsortedDeltaParser.GetDeltaAlignmentAt(id); deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; writer.Write(deltaString); } writer.Flush(); } } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="sorter">The Deltas.</param> private void WriteDelta(DeltaAlignmentSorter sorter) { TextWriter textWriterConsoleOutSave = Console.Out; StreamWriter streamWriterConsoleOut = null; try { using (var reads = File.OpenRead(this.FilePath[1])) using (var unsortedDeltas = File.OpenRead(UnsortedDeltaFile)) using (var sequenceParser = new FastASequencePositionParser(reads, true)) using (var unsortedDeltaParser = new DeltaAlignmentParser(unsortedDeltas, sequenceParser)) { if (!string.IsNullOrEmpty(this.OutputFile)) { streamWriterConsoleOut = new StreamWriter(this.OutputFile); Console.SetOut(streamWriterConsoleOut); } long deltaPositionInFile = 0; foreach (long id in sorter.GetSortedIds()) { DeltaAlignment deltaAlignment = unsortedDeltaParser.GetDeltaAlignmentAt(id); deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; Console.Write(deltaString); } Console.Out.Flush(); } } finally { if (streamWriterConsoleOut != null) streamWriterConsoleOut.Dispose(); Console.SetOut(textWriterConsoleOutSave); } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="sorter">Sorter instance.</param> /// <param name="unsortedDeltaFilename">Unsorted Delta Filename.</param> /// <param name="queryParser">Query/Read parser</param> /// <param name="outputfilename">Output file name.</param> private static void WriteSortedDelta(DeltaAlignmentSorter sorter, string unsortedDeltaFilename, FastASequencePositionParser queryParser, string outputfilename) { using (var unsortedReads = File.OpenRead(unsortedDeltaFilename)) using (DeltaAlignmentParser unsortedDeltaParser = new DeltaAlignmentParser(unsortedReads, queryParser)) { TextWriter textWriterConsoleOutSave = Console.Out; StreamWriter streamWriterConsoleOut = null; try { if (!string.IsNullOrEmpty(outputfilename)) { Output.WriteLine(OutputLevel.Required); streamWriterConsoleOut = new StreamWriter(outputfilename); Console.SetOut(streamWriterConsoleOut); } long deltaPositionInFile = 0; foreach (long id in sorter.GetSortedIds()) { DeltaAlignment deltaAlignment = unsortedDeltaParser.GetDeltaAlignmentAt(id); deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; Console.Write(deltaString); } Console.Out.Flush(); } finally { if (streamWriterConsoleOut != null) streamWriterConsoleOut.Dispose(); Console.SetOut(textWriterConsoleOutSave); } } }