/// <summary>
/// Assembles the sequences and returns the string that can be placed in a CSV output report.
/// </summary>
/// <returns></returns>
public string AssembleSequencesReturningString()
{
string toReturn = "No String Set";
TimeSpan algorithmSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo refFileinfo = new FileInfo(this.Filename);
long refFileLength = refFileinfo.Length;
runAlgorithm.Restart();
IEnumerable <ISequence> reads = this.ParseFile();
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Information, StaticResources.AssemblyStarting);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed read file: {0}", Path.GetFullPath(this.Filename));
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);
}
using (MitoPaintedAssembler assembler = new MitoPaintedAssembler())
{
assembler.AllowErosion = true;
//assembler.ReferenceGenomeFile = ReferenceGenome;
assembler.DiagnosticFileOutputPrefix = DiagnosticFilePrefix;
Console.WriteLine("Prefix is: " + assembler.DiagnosticFileOutputPrefix);
Console.WriteLine("Diagnostic Information On: " + assembler.OutputDiagnosticInformation.ToString());
assembler.StatusChanged += this.AssemblerStatusChanged;
assembler.AllowErosion = this.AllowErosion;
assembler.AllowKmerLengthEstimation = this.AllowKmerLengthEstimation;
if (ContigCoverageThreshold != -1)
{
assembler.AllowLowCoverageContigRemoval = true;
assembler.ContigCoverageThreshold = ContigCoverageThreshold;
}
assembler.DanglingLinksThreshold = this.DangleThreshold;
assembler.ErosionThreshold = this.ErosionThreshold;
if (!this.AllowKmerLengthEstimation)
{
assembler.KmerLength = this.KmerLength;
}
assembler.RedundantPathLengthThreshold = this.RedundantPathLengthThreshold;
runAlgorithm.Restart();
IDeNovoAssembly assembly = assembler.Assemble(reads);
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();
this.WriteContigs(assembly);
runAlgorithm.Stop();
toReturn = assembler.GetReportLine();
if (assembler.OutputDiagnosticInformation)
{
var outFile = new StreamWriter(ReportOutputPrefix + DiagnosticFilePrefix + ".csv");
outFile.WriteLine(MitoDataAssembler.AssemblyOutput.CreateHeaderLine());
outFile.WriteLine(toReturn);
outFile.Close();
}
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);
}
}
return(toReturn);
}
protected AssemblyReport CreateAssemblyAndDepthOfCoverage()
{
if (Skip_Assembly_Step)
{
return(new AssemblyReport());
}
DepthOfCoverageGraphMaker coveragePlotter = !Skip_DepthOfCoveragePlot ?
new DepthOfCoverageGraphMaker() : null;
IEnumerable <ISequence> reads = this.createSequenceProducer(this.Filename, coveragePlotter, true);
TimeSpan algorithmSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
//Step 1: Initialize assembler.
Output.WriteLine(OutputLevel.Verbose, "\nAssemblying mtDNA and obtaining depth of coverage (if asked).");
MitoPaintedAssembler.StatusChanged += this.StatusChanged;
MitoPaintedAssembler assembler = new MitoPaintedAssembler()
{
DiagnosticFileOutputPrefix = DiagnosticFilePrefix,
AllowErosion = AllowErosion,
AlternateMinimumNodeCount = MinimumNodeCount,
DanglingLinksThreshold = DangleThreshold,
ErosionThreshold = ErosionThreshold,
AllowKmerLengthEstimation = AllowKmerLengthEstimation,
RedundantPathLengthThreshold = RedundantPathLengthThreshold,
OutputIntermediateGraphSteps = OutputIntermediateGraphSteps,
NoContigOutput = NoContigOutput,
ForceSqrtThreshold = ForceSqrtThreshold
};
if (ContigCoverageThreshold != -1)
{
assembler.AllowLowCoverageContigRemoval = true;
assembler.ContigCoverageThreshold = ContigCoverageThreshold;
}
if (!this.AllowKmerLengthEstimation)
{
assembler.KmerLength = this.KmerLength;
}
//Step 2: Assemble
runAlgorithm.Restart();
var assembly = assembler.Assemble(reads);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "\tCompute time: {0}", runAlgorithm.Elapsed);
}
//Step 3: Report
if (!NoContigOutput)
{
runAlgorithm.Restart();
this.writeContigs(assembly);
runAlgorithm.Stop();
}
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "\tWrite contigs time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, "\tTotal assembly runtime: {0}", algorithmSpan);
}
if (coveragePlotter != null)
{
coveragePlotter.OutputCoverageGraphAndCSV(DiagnosticFilePrefix);
}
return(assembler.GetReport());
}