public ClassificationBlockProvider(GeminiOptions geminiOptions, string chrom, ConcurrentDictionary <string, int> progressTracker,
ConcurrentDictionary <PairClassification, int> categoryLookup, PairResultActionBlockFactoryProvider actionBlockFactoryProvider,
IAggregateRegionProcessor aggregateRegionProcessor, bool lightDebug, PairResultBatchBlockFactory batchBlockFactory, IBinEvidenceFactory binEvidenceFactory, List <PairClassification> categoriesForRealignment, int maxDegreeOfParallelism)
{
_geminiOptions = geminiOptions;
_chrom = chrom;
_progressTracker = progressTracker;
_categoryLookup = categoryLookup;
_maxDegreeOfParallelism = maxDegreeOfParallelism;
_actionBlockFactoryProvider = actionBlockFactoryProvider;
_aggregateRegionProcessor = aggregateRegionProcessor;
_lightDebug = lightDebug;
_binEvidenceFactory = binEvidenceFactory;
_categoriesForRealignment = categoriesForRealignment;
_batchBlockFactory = batchBlockFactory;
}
public IClassificationBlockProvider GetBlockProvider(Dictionary <int, string> refIdMapping, string chrom,
IWriterSource writerSource, ConcurrentDictionary <string, int> progressTracker,
ConcurrentDictionary <PairClassification, int> categoryLookup, ConcurrentDictionary <string, IndelEvidence> masterIndelLookup,
ConcurrentDictionary <HashableIndel, int[]> masterOutcomesLookup,
ConcurrentDictionary <HashableIndel, int> masterFinalIndels, ChrReference chrReference)
{
var actionBlockFactoryProvider = new PairResultActionBlockFactoryProvider(writerSource, _geminiOptions.Debug,
_geminiOptions.LightDebug, chrom, _geminiSampleOptions.RefId.Value, _maxDegreeOfParallelism,
_stitcherOptions.FilterForProperPairs, _geminiOptions.MessySiteWidth, progressTracker, categoryLookup);
var aggregateProcessor = new AggregateRegionProcessor(chrReference, refIdMapping,
_bamRealignmentFactory, _geminiOptions, _geminiFactory, chrom, _dataSourceFactory, _realignmentOptions, masterIndelLookup, masterOutcomesLookup, masterFinalIndels, _realignmentOptions.CategoriesForRealignment, progressTracker);
var batchBlockFactory = new PairResultBatchBlockFactory(_geminiOptions.ReadCacheSize / 5);
return(new ClassificationBlockProvider(_geminiOptions, chrom, progressTracker, categoryLookup, actionBlockFactoryProvider, aggregateProcessor,
_geminiOptions.LightDebug, batchBlockFactory, new BinEvidenceFactory(_geminiOptions, _geminiSampleOptions), _realignmentOptions.CategoriesForRealignment, _maxDegreeOfParallelism));
}