public PairResultActionBlockFactory(IWriterSource writerSource, bool debug, bool lightDebug, string chrom,
int refId, int maxDegreeOfParallelism, bool filterForProperPairs, int messySiteWidth,
ConcurrentDictionary <string, int> progressTracker, ConcurrentDictionary <PairClassification, int> categoryLookup,
int startPosition, int endPosition, int adjustedStartPosition,
ConcurrentDictionary <int, uint> totalBinCounts, ConcurrentDictionary <int, uint> singleMismatchBinCounts, int numBins,
ConcurrentDictionary <Task, int> allToWaitFor)
{
_writerSource = writerSource;
_debug = debug;
_lightDebug = lightDebug;
_chrom = chrom;
_refId = refId;
_maxDegreeOfParallelism = maxDegreeOfParallelism;
_filterForProperPairs = filterForProperPairs;
_messySiteWidth = messySiteWidth;
_progressTracker = progressTracker;
_categoryLookup = categoryLookup;
_startPosition = startPosition;
_endPosition = endPosition;
_adjustedStartPosition = adjustedStartPosition;
_totalBinCounts = totalBinCounts;
_singleMismatchBinCounts = singleMismatchBinCounts;
_numBins = numBins;
_allToWaitFor = allToWaitFor;
}
public PairResultActionBlockFactoryProvider(IWriterSource writerSource, bool debug, bool lightDebug, string chrom, int refId, int maxDegreeOfParallelism, bool filterForProperPairs, int messySiteWidth, ConcurrentDictionary <string, int> progressTracker, ConcurrentDictionary <PairClassification, int> categoryLookup)
{
_writerSource = writerSource;
_debug = debug;
_lightDebug = lightDebug;
_chrom = chrom;
_refId = refId;
_maxDegreeOfParallelism = maxDegreeOfParallelism;
_filterForProperPairs = filterForProperPairs;
_messySiteWidth = messySiteWidth;
_progressTracker = progressTracker;
_categoryLookup = categoryLookup;
}
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));
}
private static void WriteAlignments(string chrom, IWriterSource writerSource, PairClassification classification,
List <BamAlignment> alignments)
{
var idNum = Thread.CurrentThread.ManagedThreadId;
var writerHandle = writerSource.BamWriterHandle(chrom, classification, idNum);
var numAlignmentsWritten = 0;
foreach (var alignment in alignments)
{
if (alignment == null)
{
continue;
}
numAlignmentsWritten++;
writerHandle.WriteAlignment(alignment);
}
alignments.Clear();
writerSource.DoneWithWriter(chrom, classification, idNum, numAlignmentsWritten, writerHandle);
}
