/// <summary>
/// Disposes the underlaying streams used.
/// </summary>
/// <param name="disposing">Flag to indicate whether it is called from dispose method or not.</param>
protected virtual void Dispose(bool disposing)
{
if (this.deltaAlignmentParser != null)
{
this.deltaAlignmentParser.Dispose();
this.deltaAlignmentParser = null;
}
if (this.fastASequencePositionParser != null)
{
if (disposeFastASequencePositionParser)
{
this.fastASequencePositionParser.Dispose();
}
this.fastASequencePositionParser = null;
}
if (this.collectionFileReader != null)
{
this.collectionFileReader.Dispose();
this.collectionFileReader = null;
}
if (File.Exists(this.collectionFile))
{
File.Delete(this.collectionFile);
}
if (disposing)
{
this.readBuffer = null;
}
}
/// <summary>
/// Disposes the underlying streams used.
/// </summary>
/// <param name="disposing">Flag to indicate whether it is called from dispose method or not.</param>
protected virtual void Dispose(bool disposing)
{
if (disposing)
{
if (this.DeltaAlignmentParser != null)
{
this.DeltaAlignmentParser.Dispose();
this.DeltaAlignmentParser = null;
}
if (this._fastASequencePositionParser != null)
{
if (_disposeFastASequencePositionParser)
{
this._fastASequencePositionParser.Dispose();
}
this._fastASequencePositionParser = null;
}
if (this._collectionFileReader != null)
{
this._collectionFileReader.Dispose();
this._collectionFileReader = null;
}
this._readBuffer = null;
}
// Delete the collection file on Dispose or GC.
if (File.Exists(this._collectionFile))
{
File.Delete(this._collectionFile);
}
}
/// <summary>
/// Initializes a new instance of the DeltaAlignmentCollection class.
/// </summary>
/// <param name="deltaAlignmentFilename">Delta alignment file name.</param>
/// <param name="readsFilename">Query/Reads filename.</param>
public DeltaAlignmentCollection(string deltaAlignmentFilename, string readsFilename)
{
this.DeltaAlignmentFilename = deltaAlignmentFilename;
this.QueryFilename = readsFilename;
this.fastASequencePositionParser = new FastASequencePositionParser(this.QueryFilename, true);
this.deltaAlignmentParser = new DeltaAlignmentParser(this.DeltaAlignmentFilename, this.fastASequencePositionParser);
this.collectionFile = Guid.NewGuid().ToString();
this.collectionFileReader = new FileStream(this.collectionFile, FileMode.Create, FileAccess.ReadWrite);
this.LoadAllFromFile();
}
/// <summary>
/// Initializes a new instance of the DeltaAlignmentCollection class.
/// </summary>
/// <param name="deltaAlignmentFilename">Delta alignment file name.</param>
/// <param name="fastASequencePositionParser">Query/Reads filename.</param>
public DeltaAlignmentCollection(string deltaAlignmentFilename, FastASequencePositionParser fastASequencePositionParser)
{
if (fastASequencePositionParser == null)
{
throw new ArgumentNullException("fastASequencePositionParser");
}
this.disposeFastASequencePositionParser = false;
this.DeltaAlignmentFilename = deltaAlignmentFilename;
this.QueryFilename = fastASequencePositionParser.Filename;
this.fastASequencePositionParser = fastASequencePositionParser;
this.deltaAlignmentParser = new DeltaAlignmentParser(this.DeltaAlignmentFilename, this.fastASequencePositionParser);
this.collectionFile = Guid.NewGuid().ToString();
this.collectionFileReader = new FileStream(this.collectionFile, FileMode.Create, FileAccess.ReadWrite);
this.LoadAllFromFile();
}
/// <summary>
/// Disposes the underlying streams used.
/// </summary>
/// <param name="disposing">Flag to indicate whether it is called from dispose method or not.</param>
protected virtual void Dispose(bool disposing)
{
if (disposing)
{
if (this.DeltaAlignmentParser != null)
{
this.DeltaAlignmentParser.Dispose();
this.DeltaAlignmentParser = null;
}
if (this.fastASequencePositionParser != null)
{
if (this.disposeFastASequencePositionParser)
{
this.fastASequencePositionParser.Dispose();
}
this.fastASequencePositionParser = null;
}
if (this.collectionFileReader != null)
{
this.collectionFileReader.Dispose();
this.collectionFileReader = null;
}
this.readBuffer = null;
}
}
/// <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="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">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);
}
}
}