/// <summary>
/// Resolve ambiguity in the delta alignments.
/// </summary>
public void ResolveAmbiguity()
{
TimeSpan repeatResolutionSpan = new TimeSpan();
Stopwatch runRepeatResolution = new Stopwatch();
runRepeatResolution.Restart();
FileInfo inputFileinfo = new FileInfo(this.FilePath[1]);
long inputFileLength = inputFileinfo.Length;
runRepeatResolution.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Query FastA file: {0}", Path.GetFullPath(this.FilePath[1]));
Console.Error.WriteLine(" Read/Processing time: {0}", runRepeatResolution.Elapsed);
Console.Error.WriteLine(" File Size : {0}", inputFileLength);
}
inputFileinfo = new FileInfo(this.FilePath[0]);
inputFileLength = inputFileinfo.Length;
runRepeatResolution.Restart();
DeltaAlignmentSorter sorter = null;
using (var alignmentStream = File.OpenRead(this.FilePath[0]))
using (var readStream = File.OpenRead(this.FilePath[1]))
using (DeltaAlignmentCollection deltaCollection = new DeltaAlignmentCollection(alignmentStream, readStream))
{
runRepeatResolution.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed DeltaAlignment file: {0}", Path.GetFullPath(this.FilePath[0]));
Console.Error.WriteLine(" Read/Processing time: {0}", runRepeatResolution.Elapsed);
Console.Error.WriteLine(" File Size : {0}", inputFileLength);
}
runRepeatResolution.Restart();
IEnumerable <DeltaAlignment> outputDeltas = RepeatResolver.ResolveAmbiguity(deltaCollection);
sorter = new DeltaAlignmentSorter();
WriteUnsortedDelta(outputDeltas, sorter);
}
runRepeatResolution.Stop();
repeatResolutionSpan = repeatResolutionSpan.Add(runRepeatResolution.Elapsed);
runRepeatResolution.Restart();
this.WriteDelta(sorter);
runRepeatResolution.Stop();
if (this.Verbose)
{
Console.Error.WriteLine(" Compute time: {0}", repeatResolutionSpan);
Console.Error.WriteLine(" Write() time: {0}", runRepeatResolution.Elapsed);
}
}
/// <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);
}
}