/// <summary>
/// Refine layout in the delta alignments.
/// </summary>
public void RefineLayout()
{
TimeSpan timeSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
runAlgorithm.Restart();
FileInfo inputFileinfo = new FileInfo(this.FilePath[1]);
long inputFileLength = inputFileinfo.Length;
FastASequencePositionParser queryParser;
using (var input = File.OpenRead(FilePath[1]))
{
queryParser = new FastASequencePositionParser(input, true);
queryParser.CacheSequencesForRandomAccess();
}
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed Query FastA file: {0}", Path.GetFullPath(this.FilePath[1]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time : {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", inputFileLength);
}
inputFileinfo = new FileInfo(this.FilePath[0]);
inputFileLength = inputFileinfo.Length;
runAlgorithm.Restart();
using (var input = File.OpenRead(FilePath[0]))
using (DeltaAlignmentCollection deltaCollection = new DeltaAlignmentCollection(input, queryParser))
{
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed DeltaAlignment file: {0}", Path.GetFullPath(this.FilePath[0]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time : {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", inputFileLength);
}
runAlgorithm.Restart();
IEnumerable <DeltaAlignment> result = LayoutRefiner.RefineLayout(deltaCollection);
DeltaAlignmentSorter sorter = new DeltaAlignmentSorter();
WriteDelta(result, sorter, UnsortedLayoutRefinmentOutputFilename);
runAlgorithm.Stop();
timeSpan = timeSpan.Add(runAlgorithm.Elapsed);
runAlgorithm.Restart();
WriteSortedDelta(sorter, UnsortedLayoutRefinmentOutputFilename, queryParser, this.OutputFile);
runAlgorithm.Stop();
}
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Compute time: {0}", timeSpan);
Output.WriteLine(OutputLevel.Verbose, "Write time: {0}", runAlgorithm.Elapsed);
}
}
/// <summary>
/// Refine layout in the delta alignments.
/// </summary>
public void RefineLayout()
{
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();
LayoutRefiner.RefineLayout(deltas);
runAlgorithm.Stop();
timeSpan = timeSpan.Add(runAlgorithm.Elapsed);
runAlgorithm.Restart();
this.WriteDelta(deltas);
runAlgorithm.Stop();
if (this.Verbose)
{
Console.WriteLine(" Compute time: {0}", timeSpan);
Console.WriteLine(" Write() time: {0}", runAlgorithm.Elapsed);
}
}