public void Execute() { var readStatuses = new ReadStatusCounter(); var pairHandler = CreatePairHandler(readStatuses); var stitcherPairFilter = new StitcherPairFilter(_options.FilterDuplicates, _options.FilterForProperPairs, CreateDuplicateIdentifier(), readStatuses, minMapQuality: _options.FilterMinMapQuality); Logger.WriteToLog(string.Format("Beginning execution of {0}.", _inBam + (_chrFilter != null ? ":" + _chrFilter : ""))); using (var bamWriter = CreateBamWriter()) { using (var bamReader = CreateBamReader()) { var rewriter = new BamRewriter(bamReader, bamWriter, stitcherPairFilter, pairHandler, bufferSize: 100000, getUnpaired: _options.KeepUnpairedReads, chrFilter: _chrFilter); rewriter.Execute(); } } foreach (var readStatus in readStatuses.GetReadStatuses()) { Logger.WriteToLog((_chrFilter ?? "") + " STATUSCOUNT " + readStatus.Key + ": " + readStatus.Value); } if (_options.Debug || _options.DebugSummary) { foreach (var readStatus in readStatuses.GetDebugReadStatuses()) { Logger.WriteToLog((_chrFilter ?? "") + " STATUSCOUNT " + readStatus.Key + ": " + readStatus.Value); } } Logger.WriteToLog(string.Format("Done writing filtered bam at '{0}'.", _outBam)); }
public void Execute() { var readStatuses = new ReadStatusCounter(); var pairHandlers = CreatePairHandlers(readStatuses, _options.NumThreads); var stitcherPairFilter = new StitcherPairFilter(_options.FilterDuplicates, _options.FilterForProperPairs, CreateDuplicateIdentifier(), readStatuses, minMapQuality: _options.FilterMinMapQuality, filterPairUnmapped: _options.FilterPairUnmapped, filterPairLowMapQ: _options.FilterPairLowMapQ); BlockingCollection <Task> taskQueue = null; ThreadPool threadPool = null; if (_options.NumThreads > 1) { taskQueue = new BlockingCollection <Task>(4 * _options.NumThreads); threadPool = new ThreadPool(taskQueue, _options.NumThreads); } Logger.WriteToLog(string.Format("Beginning execution of {0}.", _inBam + (_chrFilter != null ? ":" + _chrFilter : ""))); using (var bamWriter = CreateBamWriter()) { using (var bamReader = CreateBamReader()) { var rewriter = new BamRewriter(bamReader, bamWriter, stitcherPairFilter, pairHandlers, taskQueue, getUnpaired: _options.KeepUnpairedReads, chrFilter: _chrFilter); rewriter.Execute(); } threadPool?.RunToCompletion(); foreach (var pairHandler in pairHandlers) { pairHandler.Finish(); } Logger.WriteToLog("Finished stitching. Starting sort and write."); bamWriter.Flush(); } foreach (var readStatus in readStatuses.GetReadStatuses()) { Logger.WriteToLog((_chrFilter ?? "") + " STATUSCOUNT " + readStatus.Key + ": " + readStatus.Value); } if (_options.Debug || _options.DebugSummary) { foreach (var readStatus in readStatuses.GetDebugReadStatuses()) { Logger.WriteToLog((_chrFilter ?? "") + " STATUSCOUNT " + readStatus.Key + ": " + readStatus.Value); } } Logger.WriteToLog(string.Format("Done writing filtered bam at '{0}'.", _outBam)); }
public void AddStatusCount() { var counter = new ReadStatusCounter(); var handler = new DebugSummaryStatusHandler(counter); handler.AddStatusCount("x"); var statuses = counter.GetReadStatuses(); Assert.Equal(1.0, statuses.Count); Assert.Equal(1, statuses["x"]); handler.AddStatusCount("y"); statuses = counter.GetReadStatuses(); Assert.Equal(2, statuses.Count); Assert.Equal(1, statuses["x"]); Assert.Equal(1, statuses["y"]); handler.AddStatusCount("x"); statuses = counter.GetReadStatuses(); Assert.Equal(2, statuses.Count); Assert.Equal(2, statuses["x"]); Assert.Equal(1, statuses["y"]); }