public ReadPair TryPair(BamAlignment alignment)
{
if (_readsProcessed % 100000 == 0)
{
LogStatus(alignment.RefID + ":" + alignment.Position);
}
_readsProcessed++;
LastRefId = alignment.RefID;
var readIndexer = ReadIndexer(alignment);
// Check if this read should be blacklisted
if (ShouldBlacklistReadIndexer(alignment))
{
_blacklistedReads.Add(readIndexer);
}
// If this read is in the blacklist, or is a read that should be "aggressively" skipped, skip the read. If we've already started tracking a mate, remove it from the mate lookup.
if (ShouldSkipAndRemoveWaitingMates(alignment) || _blacklistedReads.Contains(readIndexer))
{
_readsAggressivelySkipped++;
if (_readsWaitingForMate.ContainsKey(readIndexer))
{
_readsWaitingForMate.Remove(readIndexer);
}
return(null);
}
if (ShouldSkipRead(alignment))
{
_readsSkipped++;
return(null);
}
if (!_readsWaitingForMate.ContainsKey(readIndexer))
{
// TODO do we really need to create a new copy here? I think we're already doing it later
_readsWaitingForMate.Add(readIndexer, new ReadPair(new BamAlignment(alignment), readIndexer, GetReadNumber(alignment)));
return(null);
}
else
{
var readPair = _readsWaitingForMate[readIndexer];
readPair.AddAlignment(alignment, GetReadNumber(alignment));
if (!readPair.IsComplete(_requireSupplementaries) || _pairEvaluator.TreatReadPairAsIncomplete(readPair))
{
return(null);
}
_pairsProcessed++;
// Check pair and either skip or return pair
var shouldSkip = ShouldSkipPair(readPair);
if (!shouldSkip || _removeFailedPairs)
{
_readsWaitingForMate.Remove(readIndexer); // If succeeded, no longer waiting for mate; if failed and we're being strict on failures, remove
}
if (ShouldWhitelistReadIndexer(alignment, shouldSkip))
{
_whitelistedReads.Add(readIndexer);
}
if (shouldSkip)
{
_pairsSkipped++;
}
else
{
_pairsPaired++;
}
return(shouldSkip ? null : readPair);
}
}
public ReadPair TryPair(BamAlignment alignment)
{
if (_readsProcessed % 100000 == 0)
{
OnLog(string.Format("At {6}:{7}. Processed {0} reads and {4} pairs so far. {1} skipped, {2} pairs skipped, {5} pairs paired, {3} currently waiting for mate",
_readsProcessed, _readsSkipped, _pairsSkipped, _readsWaitingForMate.Keys.Count, _pairsProcessed, _pairsPaired, alignment.RefID, alignment.Position));
}
_readsProcessed++;
LastRefId = alignment.RefID;
// Check if this read should be blacklisted
if (ShouldBlacklistReadIndexer(alignment))
{
_blacklistedReads.Add(ReadIndexer(alignment));
}
// If this read is in the blacklist, skip the read. If we've already started tracking a mate, remove it from the mate lookup.
if (_blacklistedReads.Contains(ReadIndexer(alignment)))
{
_readsSkipped++;
if (_readsWaitingForMate.ContainsKey(ReadIndexer(alignment)))
{
_readsWaitingForMate.Remove(ReadIndexer(alignment));
}
return(null);
}
if (ShouldSkipRead(alignment))
{
_readsSkipped++;
return(null);
}
if (!_readsWaitingForMate.ContainsKey(ReadIndexer(alignment)))
{
_readsWaitingForMate.Add(ReadIndexer(alignment), new ReadPair(new BamAlignment(alignment), ReadIndexer(alignment), GetReadNumber(alignment)));
return(null);
}
else
{
var readPair = _readsWaitingForMate[ReadIndexer(alignment)];
readPair.AddAlignment(alignment, GetReadNumber(alignment));
if (!readPair.IsComplete() || _pairEvaluator.TreatReadPairAsIncomplete(readPair))
{
return(null);
}
_pairsProcessed++;
// Check pair and either skip or return pair
var shouldSkip = ShouldSkipPair(readPair);
if (!shouldSkip || _removeFailedPairs)
{
_readsWaitingForMate.Remove(ReadIndexer(alignment)); // If succeeded, no longer waiting for mate; if failed and we're being strict on failures, remove
}
if (ShouldWhitelistReadIndexer(alignment, shouldSkip))
{
_whitelistedReads.Add(ReadIndexer(alignment));
}
if (shouldSkip)
{
_pairsSkipped++;
}
else
{
_pairsPaired++;
}
return(shouldSkip ? null : readPair);
}
}