public StitchingResult TryStitch(AlignmentSet set)
{
try
{
if (set.PartnerRead1 == null || set.PartnerRead2 == null)
{
throw new ArgumentException("Set has missing read.");
}
if (IsStitchable(set))
{
// Assumption is that exactly one read is first mate
var r1IsFirstMate = !set.PartnerRead2.IsFirstMate;
// Assumption is that exactly one read is forward and one read is reverse, and each component read is only one direction
// GetStitchedCigar returns null if cigars can't possibly agree
var stitchingInfo = _cigarReconciler.GetStitchedCigar(set.PartnerRead1.CigarData,
set.PartnerRead1.Position,
set.PartnerRead2.CigarData, set.PartnerRead2.Position,
set.PartnerRead1.SequencedBaseDirectionMap.First() == DirectionType.Reverse, set.IsOutie, set.PartnerRead1.Sequence, set.PartnerRead2.Sequence, set.PartnerRead1.Qualities, set.PartnerRead2.Qualities, r1IsFirstMate);
if (stitchingInfo != null && stitchingInfo.NumDisagreeingBases + (_countNsTowardNumDisagreeingBases ? stitchingInfo.NumNDisagreements : 0) > _thresholdNumDisagreeingBases)
{
stitchingInfo = null;
}
if (stitchingInfo != null)
{
var stitchedCigar = stitchingInfo.StitchedCigar;
if (stitchedCigar == null)
// there's an overlap but we can't figure out the cigar - TODO revisit
{
AddDebugStatusCount(ReadsOverlapButWeCanTFigureOutTheCigar);
//_statusCounter.AddDebugStatusCount(ReadsOverlapButWeCanTFigureOutTheCigar);
return(new StitchingResult(false, stitchingInfo.NumDisagreeingBases, stitchingInfo.NumDisagreeingBases, stitchingInfo.NumNDisagreements));
}
// Returns null if unable to generate consensus
var mergedRead = stitchingInfo.IsSimple ? _readMerger.GenerateConsensusRead(set.PartnerRead1, set.PartnerRead2, stitchingInfo, set.IsOutie) :
_readMerger.GenerateConsensusRead(set.PartnerRead1, set.PartnerRead2,
stitchingInfo, set.IsOutie);
if (mergedRead != null)
{
mergedRead.BamAlignment.RefID = set.PartnerRead1.BamAlignment.RefID;
mergedRead.IsDuplex = set.PartnerRead1.IsDuplex || set.PartnerRead2.IsDuplex;
mergedRead.CigarDirections = stitchingInfo.StitchedDirections;
mergedRead.BamAlignment.MapQuality = Math.Max(set.PartnerRead1.MapQuality,
set.PartnerRead2.MapQuality);
if (_dontStitchHomopolymerBridge)
{
var bridgeAnchored = stitchingInfo.IsSimple ?
OverlapEvaluator.BridgeAnchored(stitchingInfo.OverlapBases) : OverlapEvaluator.BridgeAnchored(mergedRead);
if (!bridgeAnchored)
{
AddDebugStatusCount(OverlappingBasesAreRepeatCannotReliablyStitch);
//_statusCounter.AddDebugStatusCount(OverlappingBasesAreRepeatCannotReliablyStitch);
return(new StitchingResult(false, stitchingInfo.NumAgreements, stitchingInfo.NumDisagreeingBases, stitchingInfo.NumNDisagreements));
}
}
set.ReadsForProcessing.Add(mergedRead);
AddDebugStatusCount(ReadsSuccesfullyMerge);
//_statusCounter.AddDebugStatusCount(ReadsSuccesfullyMerge);
return(new StitchingResult(true, stitchingInfo.NumAgreements, stitchingInfo.NumDisagreeingBases, stitchingInfo.NumNDisagreements));
}
}
}
// If we didn't return true already, stitching failed.
if (_debug)
{
Logger.WriteToLog("Stitching failed on read " + set.PartnerRead1.Name);
}
if (_nifyUnstitchablePairs && IsStitchable(set))
{
// TODO consider removing this functionality.
// Give a merged, Nified read if the pairs are stitchable (i.e. overlap) but conflicting
try
{
var mergedRead = _readMerger.GenerateNifiedMergedRead(set, _useSoftclippedBases);
mergedRead.BamAlignment.RefID = set.PartnerRead1.BamAlignment.RefID;
mergedRead.IsDuplex = set.PartnerRead1.IsDuplex || set.PartnerRead2.IsDuplex;
mergedRead.BamAlignment.MapQuality = Math.Max(set.PartnerRead1.MapQuality,
set.PartnerRead2.MapQuality);
set.ReadsForProcessing.Add(mergedRead);
AddDebugStatusCount(UnstitchablePairNIfied);
//_statusCounter.AddDebugStatusCount(UnstitchablePairNIfied);
return(new StitchingResult(true, 0, 0, 0));
}
catch (Exception e)
{
Logger.WriteExceptionToLog(e);
//_statusCounter.AddDebugStatusCount(UnstitchablePairUnableToNifyReturnedIndividually);
AddDebugStatusCount(UnstitchablePairUnableToNifyReturnedIndividually);
set.ReadsForProcessing.Add(set.PartnerRead1);
set.ReadsForProcessing.Add(set.PartnerRead2);
}
}
else
{
AddDebugStatusCount(UnstitchablePairReturnedIndividually);
//_statusCounter.AddDebugStatusCount(UnstitchablePairReturnedIndividually);
set.ReadsForProcessing.Add(set.PartnerRead1);
set.ReadsForProcessing.Add(set.PartnerRead2);
}
return(new StitchingResult(false, 0, 0, 0));
}
catch (Exception e)
{
throw new Exception("Stitching failed for read '" + set.PartnerRead1.Name + "': " + e.Message + "..." + e.StackTrace, e.InnerException);
}
}
public bool TryStitch(AlignmentSet set)
{
if (set.PartnerRead1 == null || set.PartnerRead2 == null)
{
throw new ArgumentException("Set has missing read.");
}
if (IsStitchable(set))
{
// Assumption is that exactly one read is forward and one read is reverse, and each component read is only one direction
// GetStitchedCigar returns null if cigars can't possibly agree
var stitchingInfo = _cigarReconciler.GetStitchedCigar(set.PartnerRead1.CigarData, set.PartnerRead1.Position,
set.PartnerRead2.CigarData, set.PartnerRead2.Position,
set.PartnerRead1.SequencedBaseDirectionMap.First() == DirectionType.Reverse, set.IsOutie);
if (stitchingInfo != null)
{
var stitchedCigar = stitchingInfo.StitchedCigar;
if (stitchedCigar == null) // there's an overlap but we can't figure out the cigar - TODO revisit
{
_statusCounter.AddDebugStatusCount("Reads overlap but we can't figure out the cigar");
return(false);
}
// Returns null if unable to generate consensus
var mergedRead = _readMerger.GenerateConsensusRead(set.PartnerRead1, set.PartnerRead2, stitchingInfo, set.IsOutie);
if (mergedRead != null)
{
mergedRead.BamAlignment.RefID = set.PartnerRead1.BamAlignment.RefID;
mergedRead.IsDuplex = set.PartnerRead1.IsDuplex || set.PartnerRead2.IsDuplex;
mergedRead.CigarDirections = stitchingInfo.StitchedDirections;
mergedRead.BamAlignment.MapQuality = Math.Max(set.PartnerRead1.MapQuality, set.PartnerRead2.MapQuality);
set.ReadsForProcessing.Add(mergedRead);
_statusCounter.AddDebugStatusCount("Reads succesfully merge");
return(true);
}
}
}
// If we didn't return true already, stitching failed.
if (_debug)
{
Logger.WriteToLog("Stitching failed on read " + set.PartnerRead1.Name);
}
if (_nifyUnstitchablePairs && IsStitchable(set))
{
// Give a merged, Nified read if the pairs are stitchable (i.e. overlap) but conflicting
var mergedRead = _readMerger.GenerateNifiedMergedRead(set, _useSoftclippedBases);
mergedRead.BamAlignment.RefID = set.PartnerRead1.BamAlignment.RefID;
mergedRead.IsDuplex = set.PartnerRead1.IsDuplex || set.PartnerRead2.IsDuplex;
mergedRead.BamAlignment.MapQuality = Math.Max(set.PartnerRead1.MapQuality,
set.PartnerRead2.MapQuality);
set.ReadsForProcessing.Add(mergedRead);
_statusCounter.AddDebugStatusCount("Unstitchable pair N-ified");
return(true);
}
else
{
_statusCounter.AddDebugStatusCount("Unstitchable pair returned individually");
set.ReadsForProcessing.Add(set.PartnerRead1);
set.ReadsForProcessing.Add(set.PartnerRead2);
}
return(false);
}