/// <summary>
/// Create a sequence enumerator that filters the reads and adds them to the depth of coverage counter
/// if necessary.
/// </summary>
/// <param name="fileName">Filename to load data from</param>
/// <returns>Enumerable set of ISequence elements</returns>
private IEnumerable <CompactSAMSequence> createSequenceProducer(string fileName, DepthOfCoverageGraphMaker coveragePlotter = null, bool alsoGetNuclearHits = false)
{
if (!Skip_DepthOfCoveragePlot && !Helper.IsBAM(fileName))
{
Skip_DepthOfCoveragePlot = true;
Output.WriteLine(OutputLevel.Error, "Warning: No coverage plots can be made without an input BAM File");
}
IEnumerable <CompactSAMSequence> sequences;
if (!alsoGetNuclearHits)
{
var parser = new BAMSequenceParser(Filename);
if (ChromosomeName != string.Empty)
{
parser.ChromosomeToGet = ChromosomeName;
sequences = parser.Parse();
}
else
{
sequences = parser.Parse();
}
}
else
{
sequences = BAMNuclearChromosomeReadGenerator.GetNuclearAndMitochondrialReads(fileName);
}
//Filter by quality
return(ReadFilter.FilterReads(sequences, coveragePlotter));
}
public static IEnumerable <CompactSAMSequence> FilterReads(IEnumerable <CompactSAMSequence> preFiltered, DepthOfCoverageGraphMaker coverageCounter = null)
{
foreach (var toFilter in preFiltered)
{
if (FilterDuplicates && ((toFilter.SAMFlags & SAMFlags.Duplicate) == SAMFlags.Duplicate))
{
continue;
}
int[] vals = toFilter.GetQualityScores();
int lastAcceptableBase = (int)toFilter.Count - 1;
while (lastAcceptableBase >= 0)
{
if (vals[lastAcceptableBase] >= _trimEndQuality)
{
break;
}
lastAcceptableBase--;
}
if (lastAcceptableBase > _minReadLength)
{
//check mean
double mean = vals.Take(lastAcceptableBase + 1).Average();
if (mean > _meanRequiredQuality)
{
//only trim if necessary.
CompactSAMSequence toReturn;
if (lastAcceptableBase < (toFilter.Count - 1))
{
toFilter.TrimSequence(lastAcceptableBase + 1);
}
//Process coverage before returning the read
if (coverageCounter != null)
{
coverageCounter.ProcessCountCoverageFromSequence(toFilter);
}
yield return(toFilter);
}
}
}
}
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());
}
