private void PopulateEdgeHitsAndLogBins(int numBins, int adjustedStartPosition, int messySiteWidth, int edgeThreshold,
IBinEvidence binEvidence, Dictionary <int, int> edgeHits, Dictionary <int, int> edgeSingleMismatchHits, Dictionary <int, int> edgeIndelHits,
Dictionary <int, int> edgeMessyHits, int startPosition, BinConclusions binConclusions, UsableBins usableBins)
{
for (int binId = 0; binId < numBins; binId++)
{
var inEdge = false;
var binStart = adjustedStartPosition + (binId * messySiteWidth);
if (_geminiOptions.LogRegionsAndRealignments)
{
if (binEvidence.GetAllHits(binId) > 10 && !inEdge)
{
var binCounts =
$"{binId},{inEdge},{binStart},{binStart + messySiteWidth},{binEvidence.GetAllHits(binId)},{usableBins.IsPositionUsable(binStart)},{binEvidence.GetSingleMismatchHit(binId)}," +
$"{binConclusions.GetProbableTrueSnvRegion(binId)},{binEvidence.GetIndelHit(binId)},{binConclusions.GetIndelRegionHit(binId)}," +
$"{binEvidence.GetMessyHit(binId)},{binConclusions.GetIsMessyEnough(binId)},{binEvidence.GetForwardMessyRegionHit(binId)},{binConclusions.GetFwdMessyStatus(binId)},{binEvidence.GetReverseMessyRegionHit(binId)},{binConclusions.GetRevMessyStatus(binId)},{binEvidence.GetMapqMessyHit(binId)},{binConclusions.GetMapqMessyStatus(binId)}";
// TODO consider writing this to a proper output file
if (_geminiOptions.LogRegionsAndRealignments)
{
Logger.WriteToLog("BINCOUNTS\t" + binCounts);
}
}
}
}
}
public BinConclusions(IBinEvidence binEvidence, bool collectDepth, bool trackDirectionalMess = false, bool trackMapqMess = false)
{
_binEvidence = binEvidence;
_collectDepth = collectDepth;
var numBins = _binEvidence.NumBins;
_isMessyEnough = new SparseGroupedBoolBins(numBins);
_indelRegions = new SparseGroupedBoolBins(numBins);
if (trackDirectionalMess)
{
_fwdMessyStatus = new SparseGroupedBoolBins(numBins);
_revMessyStatus = new SparseGroupedBoolBins(numBins);
}
else
{
_fwdMessyStatus = new DummyBins <bool>();
_revMessyStatus = new DummyBins <bool>();
}
if (trackMapqMess)
{
_mapqMessyStatus = new SparseGroupedBoolBins(numBins);
}
else
{
_mapqMessyStatus = new DummyBins <bool>();
}
//if (_avoidLikelySnvs)
{
_probableTrueSnvRegions = new SparseGroupedBoolBins(numBins, 10);
}
}
public void CombineBinEvidence(IBinEvidence evidence, int binOffset = 0, int startBinInOther = 0, int endBinInOther = int.MaxValue)
{
var binEvidence = evidence as BinEvidence;
if (binEvidence == null)
{
throw new ArgumentException($"Not able to combine bin evidence between two different types.");
}
_indelHits.Merge(binEvidence._indelHits, binOffset, startBinInOther, endBinInOther);
_messyHits.Merge(binEvidence._messyHits, binOffset, startBinInOther, endBinInOther);
_singleMismatchHits.Merge(binEvidence._singleMismatchHits, binOffset, startBinInOther, endBinInOther);
AllHits.Merge(binEvidence.AllHits, binOffset, startBinInOther, endBinInOther);
_revOnlyMessyHits.Merge(binEvidence._revOnlyMessyHits, binOffset, startBinInOther, endBinInOther);
_mapqMessyHits.Merge(binEvidence._mapqMessyHits, binOffset, startBinInOther, endBinInOther);
_fwdOnlyMessyHits.Merge(binEvidence._fwdOnlyMessyHits, binOffset, startBinInOther, endBinInOther);
}
private static void AddEdgeHits(EdgeState edgeState, IBinEvidence binEvidence2, int offset, int startInOld)
{
binEvidence2.CombineBinEvidence(edgeState.BinEvidence, offset, startInOld, edgeState.BinEvidence.NumBins);
}
private List <BamAlignment> ProcessCategory(
List <PairClassification> categoriesForRealignment, IChromosomeIndelSource indelSource,
bool shouldRealignAtAll, Dictionary <HashableIndel, int[]> outcomesLookup, ref int numSkippedDueToSites,
ref int numKept, ref int numRealigned, ref int numSilenced,
List <PairResult> pairResults, PairClassification classification, IBinEvidence binEvidence,
ConcurrentDictionary <string, int> progressTracker, BinConclusions binConclusions, UsableBins usableBins, int startPosition, int endPosition)
{
var allAlignments = new List <BamAlignment>();
var isHighLikelihoodForRealign = false;
if (_geminiOptions.ForceHighLikelihoodRealigners)
{
var highLikelihoodCategories = new List <PairClassification>()
{
PairClassification.Disagree,
PairClassification.MessyStitched,
PairClassification.MessySplit,
PairClassification.UnstitchMessy,
PairClassification.UnstitchIndel
};
isHighLikelihoodForRealign = highLikelihoodCategories.Contains(classification);
}
int alignmentsCount = 0;
var doRealign = false;
ReadPairRealignerAndCombiner realignHandler = null;
var alreadyStitched = ClassificationIsStitched(classification);
var doStitch = !_geminiOptions.SkipStitching && TypeClassifier.ClassificationIsStitchable(classification);
var categoryIsRealignable = categoriesForRealignment.Contains(classification);
if (categoryIsRealignable || doStitch)
{
doRealign = true;
realignHandler = _bamRealignmentFactory.GetRealignPairHandler(doStitch,
alreadyStitched,
_realignmentOptions.PairAwareEverything ||
ClassificationIsPairAwareRealignable(classification),
_refIdMapping,
new ReadStatusCounter(), false, indelSource, _chrom, new Dictionary <string, IndelEvidence>(),
ClassificationHasIndels(classification), outcomesLookup
, SkipRestitchIfUnchanged(classification));
}
using (var snippetSource = _dataSourceFactory.CreateGenomeSnippetSource(_chrom, _chrReference))
using (var singleSnippetSource = new ReusableSnippetSource(snippetSource))
{
var nmCalculator = new NmCalculator(singleSnippetSource);
var classificationString = classification.ToString();
foreach (var pairResult in pairResults)
{
int toSilence = 0;
IEnumerable <BamAlignment> alignments;
if (!doRealign)
{
alignments = pairResult.Alignments;
}
else
{
bool doRealignPair =
shouldRealignAtAll && (isHighLikelihoodForRealign ||
(categoryIsRealignable &&
(usableBins.IsPositionUsable(pairResult.ReadPair.MinPosition) ||
usableBins.IsPositionUsable(pairResult.ReadPair.MaxPosition))));
if (!doRealignPair)
{
numSkippedDueToSites++;
}
else
{
numKept++;
}
toSilence = ReadsToSilence(classification, binConclusions, pairResult);
if (toSilence > 0)
{
numSilenced++;
}
alignments = realignHandler.ExtractReads(pairResult, nmCalculator, doRealignPair, toSilence);
if (pairResult.ReadPair.Realigned || pairResult.ReadPair.RealignedR1 ||
pairResult.ReadPair.RealignedR2)
{
numRealigned++;
}
}
var silencedR1 = (toSilence == 1 || toSilence == 3) && !pairResult.ReadPair.RealignedR1;
var silencedR2 = (toSilence == 2 || toSilence == 3) && !pairResult.ReadPair.RealignedR2;
var readTreatment = ReadTreatment(silencedR1, silencedR2, pairResult);
progressTracker.AddOrUpdate(classificationString + ":" + readTreatment, 1,
(x, currentCount) => { return(currentCount + 1); });
var alignmentsList = alignments.ToList();
foreach (var bamAlignment in alignmentsList)
{
if (_geminiOptions.LightDebug)
{
AddMdTagCountsTags(bamAlignment, pairResult);
}
bamAlignment.ReplaceOrAddStringTag("XT", readTreatment);
bamAlignment.ReplaceOrAddStringTag("XP", classificationString);
}
alignmentsCount += alignmentsList.Count();
allAlignments.AddRange(alignmentsList);
}
}
if (realignHandler != null)
{
realignHandler.Finish();
}
pairResults.Clear();
return(allAlignments);
}
