예제 #1
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 public BlockFactorySource(StitcherOptions stitcherOptions, GeminiOptions geminiOptions, Dictionary <int, string> refIdMapping, BamRealignmentFactory bamRealignmentFactory,
                           IGeminiDataSourceFactory dataSourceFactory, GeminiSampleOptions geminiSampleOptions, RealignmentOptions realignmentOptions, IGeminiFactory geminiFactory)
 {
     _stitcherOptions        = stitcherOptions;
     _geminiOptions          = geminiOptions;
     _refIdMapping           = refIdMapping;
     _bamRealignmentFactory  = bamRealignmentFactory;
     _dataSourceFactory      = dataSourceFactory;
     _geminiSampleOptions    = geminiSampleOptions;
     _realignmentOptions     = realignmentOptions;
     _geminiFactory          = geminiFactory;
     _maxDegreeOfParallelism = Math.Min(_stitcherOptions.NumThreads, Environment.ProcessorCount);
 }
예제 #2
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        public GeminiWorkflow(IGeminiDataSourceFactory dataSourceFactory,
                              IGeminiDataOutputFactory dataOutputFactory, GeminiOptions geminiOptions,
                              GeminiSampleOptions geminiSampleOptions, RealignmentOptions realignmentOptions, StitcherOptions stitcherOptions, string outputDirectory, RealignmentAssessmentOptions realignmentAssessmentOptions, IndelFilteringOptions indelFilteringOptions, ISamtoolsWrapper samtoolsWrapper)
        {
            _dataSourceFactory   = dataSourceFactory;
            _dataOutputFactory   = dataOutputFactory;
            _geminiOptions       = geminiOptions;
            _geminiSampleOptions = geminiSampleOptions;
            _realignmentOptions  = realignmentOptions;
            _samtoolsWrapper     = samtoolsWrapper;
            _stitcherOptions     = stitcherOptions ?? new StitcherOptions();

            _geminiFactory = new GeminiFactory(geminiOptions, indelFilteringOptions);
            var bamRealignmentFactory = new BamRealignmentFactory(geminiOptions,
                                                                  realignmentAssessmentOptions, stitcherOptions, realignmentOptions,
                                                                  outputDirectory);

            _bamRealignmentFactory = bamRealignmentFactory;
        }
 public AggregateRegionProcessor(ChrReference chrReference, Dictionary <int, string> refIdMapping,
                                 BamRealignmentFactory bamRealignmentFactory, GeminiOptions geminiOptions, IGeminiFactory geminiFactory,
                                 string chrom, IGeminiDataSourceFactory dataSourceFactory, RealignmentOptions realignmentOptions,
                                 ConcurrentDictionary <string, IndelEvidence> masterIndelLookup,
                                 ConcurrentDictionary <HashableIndel, int[]> masterOutcomesLookup,
                                 ConcurrentDictionary <HashableIndel, int> masterFinalIndels, List <PairClassification> categoriesForRealignment, ConcurrentDictionary <string, int> progressTracker)
 {
     _chrReference          = chrReference;
     _refIdMapping          = refIdMapping;
     _bamRealignmentFactory = bamRealignmentFactory;
     _geminiOptions         = geminiOptions;
     _geminiFactory         = geminiFactory;
     _chrom                    = chrom;
     _dataSourceFactory        = dataSourceFactory;
     _realignmentOptions       = realignmentOptions;
     _masterIndelLookup        = masterIndelLookup;
     _masterOutcomesLookup     = masterOutcomesLookup;
     _masterFinalIndels        = masterFinalIndels;
     _categoriesForRealignment = categoriesForRealignment;
     _progressTracker          = progressTracker;
 }