/// <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 sequences parser.</param> /// <param name="outputfilename">Output file name.</param> public static void WriteSortedDelta(DeltaAlignmentSorter sorter, string unsortedDeltaFilename, FastASequencePositionParser queryParser, string outputfilename) { if (sorter == null) { throw new ArgumentNullException("sorter"); } using (DeltaAlignmentParser unsortedDeltaParser = new DeltaAlignmentParser(unsortedDeltaFilename, queryParser)) { using (StreamWriter writer = new StreamWriter(outputfilename)) { 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="delta">The Deltas.</param> private void WriteDelta( DeltaAlignmentSorter sorter) { FastASequencePositionParser sequenceParser = null; DeltaAlignmentParser unsortedDeltaParser = null; TextWriter textWriterConsoleOutSave = Console.Out; StreamWriter streamWriterConsoleOut = null; try { sequenceParser = new FastASequencePositionParser(this.FilePath[1], true); unsortedDeltaParser = new DeltaAlignmentParser(UnsortedDeltaFile, 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(); streamWriterConsoleOut = null; } if (sequenceParser != null) { sequenceParser.Dispose(); sequenceParser = null; } if (unsortedDeltaParser != null) { unsortedDeltaParser.Dispose(); unsortedDeltaParser = null; } 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="queryFilename">Query/read sequences filename.</param> /// <param name="outputfilename">Output file name.</param> private static void WriteSortedDelta(DeltaAlignmentSorter sorter, string unsortedDeltaFilename, FastASequencePositionParser queryParser, string outputfilename) { using (DeltaAlignmentParser unsortedDeltaParser = new DeltaAlignmentParser(unsortedDeltaFilename, queryParser)) { TextWriter textWriterConsoleOutSave = Console.Out; StreamWriter streamWriterConsoleOut = null; try { if (!string.IsNullOrEmpty(outputfilename)) { 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(); streamWriterConsoleOut = null; } Console.SetOut(textWriterConsoleOutSave); } } }