/// <summary>
/// Assemble function.
/// </summary>
/// <param name="args">Arguments to Assemble.</param>
private static void Assemble(string[] args)
{
AssembleArguments options = new AssembleArguments();
CommandLineArguments parser = new CommandLineArguments();
AddAssembleParameters(parser);
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.AssembleHelp);
Environment.Exit(-1);
}
if (options.Help)
{
DisplayErrorMessage(Resources.AssembleHelp);
}
else
{
options.AssembleSequences();
}
}
else
{
DisplayErrorMessage(Resources.AssembleHelp);
}
}
/// <summary>
/// Assemble function.
/// </summary>
/// <param name="args">Arguments to Assemble.</param>
private static void Assemble(string[] args)
{
AssembleArguments options = new AssembleArguments();
CommandLineArguments parser = new CommandLineArguments();
AddAssembleParameters(parser);
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.AssembleHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleHelp);
}
else
{
ValidateKmerLength(options.KmerLength, options.AllowKmerLengthEstimation);
if (options.Verbose)
{
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
}
else if (!options.Quiet)
{
Output.TraceLevel = OutputLevel.Information;
}
options.AssembleSequences();
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleHelp);
}
}
/// <summary>
/// Assemble function.
/// </summary>
/// <param name="args">Arguments to Assemble.</param>
private static void Assemble(string[] args)
{
AssembleArguments options = new AssembleArguments();
if (args.Length > 0 && Parser.ParseArguments(args, options))
{
if (options.Help)
{
DisplayErrorMessage(Resources.AssembleHelp);
}
else
{
options.AssembleSequences();
}
}
else
{
DisplayErrorMessage(Resources.AssembleHelp);
}
}
/// <summary>
/// Generates the Scaffold.
/// </summary>
public void GenerateScaffold()
{
Output.WriteLine(OutputLevel.Information, Resources.ScaffoldStarting);
if (this.FileNames.Length != 2)
{
Output.WriteLine(OutputLevel.Error, "\nError: A reference file and 1 query file are required.");
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
return;
}
if (!string.IsNullOrEmpty(this.CloneLibraryName))
{
CloneLibrary.Instance.AddLibrary(this.CloneLibraryName, (float)this.MeanLengthOfInsert, (float)this.StandardDeviationOfInsert);
}
TimeSpan algorithmSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo refFileinfo = null;
using (GraphScaffoldBuilder scaffoldBuilder = new GraphScaffoldBuilder())
{
refFileinfo = new FileInfo(this.FileNames[0]);
long refFileLength = refFileinfo.Length;
runAlgorithm.Restart();
IEnumerable <ISequence> contigs = AssembleArguments.ParseFile(this.FileNames[0]);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed contigs file : {0}", Path.GetFullPath(this.FileNames[0]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", refFileLength);
Output.WriteLine(OutputLevel.Verbose, " k-mer Length : {0}", this.KmerLength);
}
refFileinfo = new FileInfo(this.FileNames[1]);
refFileLength = refFileinfo.Length;
runAlgorithm.Restart();
IEnumerable <ISequence> reads = AssembleArguments.ParseFile(this.FileNames[1]);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed reads file : {0}", Path.GetFullPath(this.FileNames[1]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", refFileLength);
}
runAlgorithm.Restart();
ValidateAmbiguousReads(reads);
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Time taken for Validating reads: {0}", runAlgorithm.Elapsed);
}
runAlgorithm.Restart();
IList <ISequence> scaffolds = scaffoldBuilder.BuildScaffold(reads, contigs.ToList(), this.KmerLength, this.Depth, this.Redundancy);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Compute time: {0}", runAlgorithm.Elapsed);
}
runAlgorithm.Restart();
WriteContigs(scaffolds);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Write contigs time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, "Total runtime: {0}", algorithmSpan);
}
}
}
/// <summary>
/// Assemble function.
/// </summary>
/// <param name="args">Arguments to Assemble.</param>
private static void Assemble(string[] args)
{
AssembleArguments options = new AssembleArguments();
CommandLineArguments parser = new CommandLineArguments();
AddAssembleParameters(parser);
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.AssembleHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleHelp);
}
else
{
ValidateKmerLength(options.KmerLength, options.AllowKmerLengthEstimation);
if (options.Verbose)
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
else if (!options.Quiet)
Output.TraceLevel = OutputLevel.Information;
options.AssembleSequences();
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.AssembleHelp);
}
}
