public ValidationParser(PileupProcessorOptions options, MpileupResult result) { _options = options; _parser = options.GetPileupItemParser(false); _rdFilter = new PileupItemReadDepthFilter(options.MinimumReadDepth, options.MinimumBaseQuality); _normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal); _tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor); _result = result; }
public ValidationParser(PileupProcessorOptions options, MpileupResult result) { _options = options; _parser = options.GetPileupItemParser(false); _rdFilter = new PileupItemReadDepthFilter(options.MinimumReadDepth, options.MinimumBaseQuality); _normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal); _tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor); _result = result; }
public MpileupParser(PileupProcessorOptions options, MpileupResult result) { _options = options; _normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal); _tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor); _parser = options.GetPileupItemParser(); _result = result; if (File.Exists(_options.ExcludeBedFile)) { bedMap = new BedItemFile <BedItem>().ReadFromFile(_options.ExcludeBedFile).ToGroupDictionary(m => m.Seqname); } }
public AbstractPileupProcessor(PileupProcessorOptions options) { _options = options; }
public MpileupResultCountFormat(PileupProcessorOptions options, bool outputNotCovered) { this.options = options; this.outputNotCovered = outputNotCovered; }
public PileupProcessorSingleThread(PileupProcessorOptions options) : base(options) { }
public PileupProcessorParallelChromosome(PileupProcessorOptions options) : base(options) { }
public MpileupResultProcessor(PileupProcessorOptions options) : base(options) { _options = options; }
public PileupProcessorParallelChromosome(PileupProcessorOptions options) : base(options) { }
public PileupProcessorSingleThread(PileupProcessorOptions options) : base(options) { }
public AbstractPileupProcessor(PileupProcessorOptions options) { _options = options; }
public MpileupResultProcessor(PileupProcessorOptions options) : base(options) { _options = options; }