/// <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>
/// Resolve ambuiguity in the delta alignments.
/// </summary>
public void ResolveAmbiguity()
{
TimeSpan repeatResolutionSpan = new TimeSpan();
Stopwatch runRepeatResolution = new Stopwatch();
FileInfo inputFileinfo = new FileInfo(this.FilePath);
long inputFileLength = inputFileinfo.Length;
inputFileinfo = null;
runRepeatResolution.Restart();
DeltaAlignmentParser parser = new DeltaAlignmentParser(this.FilePath);
IList <IEnumerable <DeltaAlignment> > deltas = parser.Parse();
runRepeatResolution.Stop();
if (this.Verbose)
{
Console.WriteLine();
Console.WriteLine(" Processed DeltaAlignment file: {0}", Path.GetFullPath(this.FilePath));
Console.WriteLine(" Read/Processing time: {0}", runRepeatResolution.Elapsed);
Console.WriteLine(" File Size : {0}", inputFileLength);
}
runRepeatResolution.Restart();
List <DeltaAlignment> outputDeltas = RepeatResolver.ResolveAmbiguity(deltas);
List <DeltaAlignment> orderedOutputDeltas = outputDeltas.OrderBy(a => a.FirstSequenceStart).ToList();
runRepeatResolution.Stop();
repeatResolutionSpan = repeatResolutionSpan.Add(runRepeatResolution.Elapsed);
runRepeatResolution.Restart();
this.WriteDelta(orderedOutputDeltas);
runRepeatResolution.Stop();
if (this.Verbose)
{
Console.WriteLine(" Compute time: {0}", repeatResolutionSpan);
Console.WriteLine(" Write() time: {0}", runRepeatResolution.Elapsed);
}
}
/// <summary>
/// Refine layout in the delta alignments.
/// </summary>
public void GenerateConsensus()
{
TimeSpan timeSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo inputFileinfo = new FileInfo(this.FilePath);
long inputFileLength = inputFileinfo.Length;
inputFileinfo = null;
runAlgorithm.Restart();
DeltaAlignmentParser parser = new DeltaAlignmentParser(this.FilePath);
IList <DeltaAlignment> deltas = parser.Parse();
runAlgorithm.Stop();
if (this.Verbose)
{
Console.WriteLine();
Console.WriteLine(" Processed DeltaAlignment file: {0}", Path.GetFullPath(this.FilePath));
Console.WriteLine(" Read/Processing time: {0}", runAlgorithm.Elapsed);
Console.WriteLine(" File Size : {0}", inputFileLength);
}
runAlgorithm.Restart();
IEnumerable <ISequence> consensus = ConsensusGeneration.GenerateConsensus(deltas);
runAlgorithm.Stop();
timeSpan = timeSpan.Add(runAlgorithm.Elapsed);
runAlgorithm.Restart();
this.WriteSequences(consensus);
runAlgorithm.Stop();
if (this.Verbose)
{
Console.WriteLine(" Compute time: {0}", timeSpan);
Console.WriteLine(" Write() time: {0}", runAlgorithm.Elapsed);
}
}
/// <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);
}
}
}
