private void RecalculateIndelAndAddIfNeeded(bool allowRescue, KeyValuePair <HashableIndel, List <IndelEvidence> > indelToRecalculate,
IndelStatusCounter statusCounter, double edgeThreshold, List <PreIndel> indelsToAdd)
{
var hashable = indelToRecalculate.Key;
var indel = new PreIndel(new CandidateAllele(hashable.Chromosome, hashable.ReferencePosition,
hashable.ReferenceAllele, hashable.AlternateAllele, hashable.Type));
indel.InMulti = hashable.InMulti;
indel.OtherIndel = hashable.OtherIndel;
var metrics = new IndelEvidence();
foreach (var metricsList in indelToRecalculate.Value)
{
metrics.AddIndelEvidence(metricsList);
}
var entryIndels = ExtractIndelsFromEntry(metrics, indel.ToString() + "|" + indel.OtherIndel,
statusCounter, edgeThreshold, allowRescue, new List <PreIndel>()
{
indel
});
if (entryIndels != null)
{
indelsToAdd.AddRange(entryIndels);
}
}
private bool ShouldRemoveVariant(int observationCount, float avgAnchorLeft, float avgAnchorRight, bool isStrong,
IndelStatusCounter statusCounter, float avgQuals, float avgMess, int anchorLeft, int anchorRight, double edgeThreshold, IndelEvidence evidence)
{
if (observationCount < _foundThreshold || avgAnchorLeft < _anchorThreshold || avgAnchorRight < _anchorThreshold || avgMess > _maxMess)
{
if (isStrong)
{
evidence.Outcome = Outcome.Rescued;
statusCounter.Rescued++;
}
else
{
evidence.Outcome = Outcome.BelowThreshold;
statusCounter.BelowThreshold++;
return(true);
}
}
if (observationCount == 1 && (Math.Min(anchorLeft, anchorRight) < 5 || avgMess > 1 || avgQuals < 30))
{
evidence.Outcome = Outcome.PoorSingle;
statusCounter.PoorSingle++;
// Even if we want to allow single-observation variants to be realigned against, maybe let's avoid the really junky ones
return(true);
}
if ((observationCount <= edgeThreshold) && (avgMess > 2 || avgQuals < 25))
{
evidence.Outcome = Outcome.PoorEdge;
statusCounter.PoorEdge++;
return(true);
}
return(false);
}
public Dictionary <string, List <PreIndel> > GetRealignablePreIndels(Dictionary <string, IndelEvidence> indelStringLookup, bool allowRescue, int regionEdgeThreshold = int.MaxValue)
{
var statusCounter = new IndelStatusCounter();
var edgeThreshold = Math.Max(_foundThreshold + 1, _foundThreshold * 1.5);
var indelsToAdd = new List <PreIndel>();
var multiIndelsToRecalculate = new Dictionary <HashableIndel, List <IndelEvidence> >();
var indelsToRemove = new List <string>();
var numImmediatelySkipped = 0;
var numProcessed = 0;
// TODO different way of doing this, bc we don't use the indel after that
var indelsLookup = new Dictionary <string, List <PreIndel> >();
foreach (var key in indelStringLookup.Keys)
{
var indelMetrics = indelStringLookup[key];
var keepForNextRegion = indelMetrics.Position >= regionEdgeThreshold;
if (indelMetrics.Observations == 0 && !keepForNextRegion)
{
indelMetrics.Outcome = Outcome.LowObservations;
continue;
}
numProcessed++;
if (indelMetrics.Observations < _strictFoundThreshold && !keepForNextRegion)
{
indelMetrics.Outcome = Outcome.LowObservations;
numImmediatelySkipped++;
continue;
}
// No reputable evidence!
if (indelMetrics.ReputableSupport < 1 && !keepForNextRegion)
{
indelMetrics.Outcome = Outcome.LowReputableSupport;
numImmediatelySkipped++;
continue;
}
var entryIndelKeys = ExtractIndelsFromKeyString(key);
if (entryIndelKeys == null)
{
continue;
}
if (entryIndelKeys.Count > 1)
{
foreach (var entryIndel in entryIndelKeys)
{
var multiKey = GetHashableIndel(entryIndel);
if (!multiIndelsToRecalculate.TryGetValue(multiKey, out var existingIndelMetrics))
{
existingIndelMetrics = new List <IndelEvidence>();
multiIndelsToRecalculate[multiKey] = existingIndelMetrics;
}
existingIndelMetrics.Add(indelMetrics);
}
}
else
{
var entryIndels = ExtractIndelsFromEntry(indelMetrics, key, statusCounter, edgeThreshold,
allowRescue, entryIndelKeys);
if (entryIndels != null)
{
indelsToAdd.AddRange(entryIndels);
}
else
{
indelsToRemove.Add(key);
}
}
}
foreach (var indelToRecalculate in multiIndelsToRecalculate)
{
RecalculateIndelAndAddIfNeeded(allowRescue, indelToRecalculate, statusCounter, edgeThreshold, indelsToAdd);
}
foreach (var indel in indelsToAdd)
{
if (!indelsLookup.TryGetValue(indel.Chromosome, out var indelsForChrom))
{
indelsForChrom = new List <PreIndel>();
indelsLookup.Add(indel.Chromosome, indelsForChrom);
}
indelsForChrom.Add(indel);
}
foreach (var badIndel in indelsToRemove)
{
indelStringLookup.Remove(badIndel);
}
statusCounter.BelowThreshold += numImmediatelySkipped;
return(indelsLookup);
}
private List <PreIndel> ExtractIndelsFromEntry(IndelEvidence indelMetrics, string keyString,
IndelStatusCounter statusCounter,
double edgeThreshold, bool allowRescue, List <PreIndel> indels)
{
var indelsToAdd = new List <PreIndel>();
var observationCount = indelMetrics.Observations;
var anchorLeft = indelMetrics.LeftAnchor;
var anchorRight = indelMetrics.RightAnchor;
var mess = indelMetrics.Mess;
var quals = indelMetrics.Quality;
var fwdSupport = indelMetrics.Forward / (float)observationCount;
var reverseSupport = indelMetrics.Reverse / (float)observationCount;
var stitchedSupport = indelMetrics.Stitched / (float)observationCount;
var reputableSupportFraction = indelMetrics.ReputableSupport / (float)observationCount;
var numFromUnanchoredRepeat = indelMetrics.IsRepeat;
var numFromMateUnmapped = indelMetrics.IsSplit;
var avgAnchorLeft = anchorLeft / (float)observationCount;
var avgAnchorRight = anchorRight / (float)observationCount;
var avgQuals = quals / (float)observationCount;
var avgMess = mess / (float)observationCount;
// TODO clean this up, no more magic
bool isStrong = false;
if (allowRescue)
{
isStrong = IsStrong(avgQuals, reputableSupportFraction, avgAnchorLeft, avgMess, avgAnchorRight,
reverseSupport, observationCount, fwdSupport, keyString, stitchedSupport);
}
if (indels.Count > 2)
{
Logger.WriteToLog(
$"Can't support more than 2 indels in one read: ignoring multi-indel {keyString} (seen {observationCount} times)");
}
else if (indels.Count > 1)
{
var indel1 = GetIndelFromEntry(indels[0], anchorLeft, anchorRight, observationCount, mess, fwdSupport,
reverseSupport, reputableSupportFraction, avgQuals, stitchedSupport, numFromMateUnmapped, numFromUnanchoredRepeat);
var indel2 = GetIndelFromEntry(indels[1], anchorLeft, anchorRight, observationCount, mess, fwdSupport,
reverseSupport, reputableSupportFraction, avgQuals, stitchedSupport, numFromMateUnmapped, numFromUnanchoredRepeat);
indel1.InMulti = true;
indel2.InMulti = true;
indel1.OtherIndel = Helper.CandidateToString(indel2);
indel2.OtherIndel = Helper.CandidateToString(indel1);
indelsToAdd.Add(indel1);
indelsToAdd.Add(indel2);
}
else
{
var indel = GetIndelFromEntry(indels[0], anchorLeft, anchorRight, observationCount, mess, fwdSupport,
reverseSupport, reputableSupportFraction, avgQuals, stitchedSupport, numFromMateUnmapped, numFromUnanchoredRepeat);
indelsToAdd.Add(indel);
}
if (indels.Count == 1 && indelsToAdd[0].Length == 1 && (observationCount < _foundThreshold * 0.8 || observationCount <= 2))
{
indelMetrics.Outcome = Outcome.SuperWeakSmall;
return(null);
}
if (ShouldRemoveVariant(observationCount, avgAnchorLeft, avgAnchorRight, isStrong, statusCounter,
avgQuals,
avgMess, anchorLeft, anchorRight, edgeThreshold, indelMetrics))
{
return(null);
}
statusCounter.Kept++;
return(indelsToAdd);
}
