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);
}
public ActionBlock <PairResult[]> GetEarlyFlushBlock(PairClassification classification, bool isSingleMismatch)
{
var actBlock = new ActionBlock <PairResult[]>((p) =>
{
if (_lightDebug)
{
Logger.WriteToLog(
$"Started handling {classification} block for region {_chrom}:{_startPosition}-{_endPosition}.");
}
var toRemove2 = _allToWaitFor.Keys.Where(x => x.IsCompleted);
foreach (var task in toRemove2)
{
_allToWaitFor.TryRemove(task, out _);
}
if (_debug)
{
Console.WriteLine($"{p.Length} pairs in category {classification} in {_startPosition}-{_endPosition}");
}
var idNum = Thread.CurrentThread.ManagedThreadId;
var writerHandle = _writerSource.BamWriterHandle(_chrom, classification, _startPosition);
_categoryLookup.AddOrUpdate(classification, p.Sum(x => x.ReadPair.NumPrimaryReads),
(c, n) => { return(n + p.Sum(x => x.ReadPair.NumPrimaryReads)); });
if (_filterForProperPairs && _improperTypes.Contains(classification))
{
_progressTracker.AddOrUpdate("Skipped", p.Sum(x => x.ReadPair.NumPrimaryReads),
(c, n) => { return(n + p.Sum(x => x.ReadPair.NumPrimaryReads)); });
}
else
{
var numAlignmentsWritten = 0;
var classificationString = classification.ToString();
foreach (var pair in p)
{
if (classification != PairClassification.Duplicate)
{
// Don't add bin evidence for duplicates, may wash the signal out
BinEvidenceHelpers.AddEvidence(pair, _messySiteWidth, _adjustedStartPosition,
_totalBinCounts,
_singleMismatchBinCounts, isSingleMismatch, _numBins, _refId);
}
foreach (var alignment in pair.Alignments)
{
if (alignment == null)
{
continue;
}
alignment.ReplaceOrAddStringTag("XP", classificationString);
numAlignmentsWritten++;
if (writerHandle == null)
{
throw new Exception("This is odd, why is the handle null");
}
writerHandle.WriteAlignment(alignment);
}
}
_progressTracker.AddOrUpdate("Early Flushed", p.Sum(x => x.ReadPair.NumPrimaryReads),
(s, n) => { return(n + p.Sum(x => x.ReadPair.NumPrimaryReads)); });
_progressTracker.AddOrUpdate("Simple Alignments Written", numAlignmentsWritten,
(s, n) => { return(n + numAlignmentsWritten); });
Array.Clear(p, 0, p.Length);
_writerSource.DoneWithWriter(_chrom, classification, idNum, numAlignmentsWritten, writerHandle);
if (_lightDebug)
{
Logger.WriteToLog(
$"Done handling {classification} block for region {_chrom}:{_startPosition}-{_endPosition}.");
}
}
}, new ExecutionDataflowBlockOptions()
{
MaxDegreeOfParallelism = _maxDegreeOfParallelism, EnsureOrdered = true
});
return(actBlock);
}
