/// <summary>
/// Constructor for holding all read statistics calculated
/// from the QC analysis.
/// </summary>
/// <param name="main"></param>
public InputStatistics(Seqcos main)
{
if (main == null)
{
throw new ArgumentNullException("Seqcos");
}
this.myFilenames = main.FileList;
if (main.SequenceQc != null && main.SequenceQc.IsReady)
{
this.NumberOfReads = main.SequenceQc.Count;
this.ReadLengthMin = main.SequenceQc.ReadLengths.Min();
this.ReadLengthMax = main.SequenceQc.ReadLengths.Max();
this.ReadLengthMean = main.SequenceQc.ReadLengths.Average();
this.ReadGcContentMin = main.SequenceQc.GCContentBySequenceArray.Min();
this.ReadGcContentMax = main.SequenceQc.GCContentBySequenceArray.Max();
this.ReadGcContentMean = main.SequenceQc.GCContentBySequenceArray.Mean();
this.ReadGcContentStd = main.SequenceQc.GCContentBySequenceArray.Std();
}
if (main.QualityScoreQc != null && main.QualityScoreQc.IsReady)
{
if (this.NumberOfReads == 0)
{
this.NumberOfReads = main.QualityScoreQc.Count;
}
this.BasePhredScoreMin = main.QualityScoreQc.BaseQualityScoreMin;
this.BasePhredScoreMax = main.QualityScoreQc.BaseQualityScoreMax;
this.BasePhredScoreMean = main.QualityScoreQc.BaseQualityScoreMean;
this.ReadPhredScoreMin = main.QualityScoreQc.ReadQualityScoreMin;
this.ReadPhredScoreMax = main.QualityScoreQc.ReadQualityScoreMax;
this.ReadPhredScoreMean = main.QualityScoreQc.ReadQualityScoreMean;
this.FastQFormat = main.QualityScoreQc.FormatType.ToString();
}
}
/// <summary>
/// Controls execution of QC steps
/// </summary>
/// <param name="parser">ISequenceParser object holding the input sequence data</param>
/// <param name="filename">Input filename</param>
/// <param name="runSequenceQc">Indicates whether the sequence-level QC module should be initialized</param>
/// <param name="runQualityScoreQc">Indicates whether the quality score-level QC module should be initialized</param>
/// <param name="runBlast">Indicates whether the sequence contamination finder module should be initialized</param>
/// <param name="format">FastQ Format Type, if applicable. Otherwise use 'null'.</param>
/// <param name="dir">Output directory</param>
public Seqcos(ISequenceParser parser, string filename, bool runSequenceQc, bool runQualityScoreQc, bool runBlast, string format, string dir = null)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (filename == null)
{
throw new ArgumentNullException("filename");
}
// (deprecated) Register AssemblyResolve event handler - for dealing with Sho libaries that are located
// externally from this application's install folder
//AppDomain currentDomain = AppDomain.CurrentDomain;
//currentDomain.AssemblyResolve += new ResolveEventHandler(OnAssemblyResolveEventHandler);
this.myFilenames = new Filenames(filename, Resource.ChartFormat);
this.SelectedParser = parser;
this.OutputDirectory = (dir == null) ? Path.GetDirectoryName(filename) + @"\" + myFilenames.Prefix : dir;
//string customOutputPath = Path.GetDirectoryName(this.OutputDirectory);
this.InitialWorkingDirectory = Path.GetDirectoryName(filename);
Directory.SetCurrentDirectory(this.InitialWorkingDirectory);
if (!Directory.Exists(this.OutputDirectory))
{
Directory.CreateDirectory(this.OutputDirectory);
}
// Initialize SequenceAnalyzer
this.SequenceQc = runSequenceQc ? new SequenceAnalyzer(this.SelectedParser, myFilenames.FileName) : null;
// Initialize QualityScoreAnalyzer
if (runQualityScoreQc && !(parser is FastAParser))
{
if (format == null)
{
throw new ArgumentNullException("format");
}
FastQFormatType myFormat = BioHelper.GetQualityFormatType(format);
if (runSequenceQc && this.SequenceQc != null)
{
this.QualityScoreQc = new QualityScoreAnalyzer(this.SelectedParser, this.SequenceQc.ReadLengthMax, this.SequenceQc.Count, myFormat, myFilenames.FileName);
}
else
{
this.QualityScoreQc = new QualityScoreAnalyzer(this.SelectedParser, myFormat, myFilenames.FileName);
}
}
else
{
this.QualityScoreQc = null;
}
// Initialize ContaminationFinder
this.ContaminationFinder = runBlast ? new SequenceContaminationFinder(this.SelectedParser) : null;
this.HasPlottedSequenceStats = false;
this.HasPlottedQualityScoreStats = false;
}