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 ExecuteTest()
{
var alignmentsToRead = new List <BamAlignment>()
{
CreateAlignment("pair"),
CreateAlignment("pair2"),
CreateAlignment("single")
};
var writtenAlignments = new List <BamAlignment>();
var unpairedAlignments = new List <BamAlignment>();
var bamWriter = new Mock <IBamWriterMultithreaded>();
bamWriter.Setup(x => x.WriteAlignment(It.IsAny <BamAlignment>())).Callback <BamAlignment>((b) => writtenAlignments.Add(b));
var bamWriterHandle = new Mock <IBamWriterHandle>();
var bamWriterHandleList = new List <IBamWriterHandle>();
bamWriterHandleList.Add(bamWriterHandle.Object);
bamWriterHandle.Setup(x => x.WriteAlignment(It.IsAny <BamAlignment>())).Callback <BamAlignment>((b) => writtenAlignments.Add(b));
bamWriter.Setup(x => x.GenerateHandles()).Returns(() => { return(bamWriterHandleList); });
bamWriter.Setup(x => x.Flush());
var alignmentPairFilter = new Mock <IAlignmentPairFilter>();
alignmentPairFilter.Setup(f => f.TryPair(It.IsAny <BamAlignment>()))
.Returns <BamAlignment>((b) =>
{
if (b.Name.StartsWith("pair"))
{
var x = new ReadPair(b);
x.AddAlignment(b);
return(x);
}
unpairedAlignments.Add(b);
return(null);
}
);
alignmentPairFilter.Setup(f => f.GetFlushableUnpairedReads()).Returns(unpairedAlignments);
BlockingCollection <Task> taskQueue = new BlockingCollection <Task>();
// Create a thread pool with 1 thread. It will execute any tasks
// added to the taskQueue by the BamRewriter.
ThreadPool threadPool = new ThreadPool(taskQueue, 1);
var readPairHandler = new Mock <IReadPairHandler>();
readPairHandler.Setup(h => h.ExtractReads(It.IsAny <ReadPair>())).Returns <ReadPair>(
(p) =>
{
var list = new List <BamAlignment>();
list.AddRange(p.Read1Alignments);
list.AddRange(p.Read2Alignments);
return(list);
}
);
// Given a list of reads, should try to pair them all
// Should flush to bam once the buffer reaches the specified size
// If specifying getUnpaired = true, should also flush unpaired reads (as designated by the filter) to the bam
var bamRewriter = new BamRewriter(MockBamReader(alignmentsToRead), bamWriter.Object,
alignmentPairFilter.Object, new List <IReadPairHandler> {
readPairHandler.Object
}, taskQueue, true);
bamRewriter.Execute();
Assert.Equal(5, writtenAlignments.Count);
// Should get all of the reads flushed, regardless of buffer size
writtenAlignments.Clear();
unpairedAlignments.Clear();
bamRewriter = new BamRewriter(MockBamReader(alignmentsToRead), bamWriter.Object,
alignmentPairFilter.Object, new List <IReadPairHandler> {
readPairHandler.Object
}, taskQueue, true);
bamRewriter.Execute();
Assert.Equal(5, writtenAlignments.Count);
writtenAlignments.Clear();
unpairedAlignments.Clear();
bamRewriter = new BamRewriter(MockBamReader(alignmentsToRead), bamWriter.Object,
alignmentPairFilter.Object, new List <IReadPairHandler> {
readPairHandler.Object
}, taskQueue, true);
bamRewriter.Execute();
Assert.Equal(5, writtenAlignments.Count);
// If getUnpaired = false, should not flush unpaired reads to the bam
writtenAlignments.Clear();
unpairedAlignments.Clear();
bamRewriter = new BamRewriter(MockBamReader(alignmentsToRead), bamWriter.Object,
alignmentPairFilter.Object, new List <IReadPairHandler> {
readPairHandler.Object
}, taskQueue, false);
bamRewriter.Execute();
Assert.Equal(4, writtenAlignments.Count);
Assert.True(writtenAlignments.All(a => a.Name.StartsWith("pair")));
}
