public ExtractReadsTask(List <IReadPairHandler> pairHandlers, List <ReadPair> readPairs, List <IBamWriterHandle> bamWriterHandles, IAlignmentPairFilter filter = null) : base() { _pairHandlers = pairHandlers; _filter = filter; _readPairs = readPairs; _bamWriterHandles = bamWriterHandles; }
public BamRewriter(IBamReader bamReader, IBamWriterMultithreaded bamWriter, IAlignmentPairFilter filter, List <IReadPairHandler> pairHandlers, BlockingCollection <Task> taskQueue, bool getUnpaired = false, string chrFilter = null) { _bamReader = bamReader; _bamWriter = bamWriter; _filter = filter; _pairHandlers = pairHandlers; _getUnpaired = getUnpaired; _chrFilter = chrFilter; _taskQueue = taskQueue; }
public BamRewriter(IBamReader bamReader, IBamWriter bamWriter, IAlignmentPairFilter filter, IReadPairHandler pairHandler, long?bufferSize = 100000, bool getUnpaired = false, string chrFilter = null) { _bamReader = bamReader; _bamWriter = bamWriter; _filter = filter; _pairHandler = pairHandler; _bufferSize = bufferSize; _getUnpaired = getUnpaired; _chrFilter = chrFilter; _alignmentBuffer = new List <BamAlignment>(); OnLog = message => Console.WriteLine(message); }
public PairFilterReadPairSource(IBamReader bamReader, ReadStatusCounter readStatuses, bool skipAndRemoveDuplicates, IAlignmentPairFilter filter, int?refId = null, int?expectedFragmentLength = null, bool filterForProperPairs = false) { _bamReader = bamReader; _readStatuses = readStatuses; _skipAndRemoveDuplicates = skipAndRemoveDuplicates; if (refId != null) { _applyChrFilter = true; _refId = refId.Value; _bamReader.Jump(_refId, 0); } _filter = filter; _filterForProperPairs = filterForProperPairs; if (expectedFragmentLength != null) { _considerInsertSize = true; _expectedFragmentLength = expectedFragmentLength.Value; } }