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"]);
}