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 void ProcessRegions(int messySiteThreshold, double imperfectFreqThreshold, int regionDepthThreshold,
double indelRegionFreqThreshold, int binsToExtendTo, float directionalMessThreshold)
{
for (int i = 0; i < _binEvidence.NumBins; i++)
{
if (_collectDepth && _binEvidence.GetAllHits(i) == 0)
{
continue;
}
if (!_collectDepth && _binEvidence.GetMessyHit(i) == 0 && _binEvidence.GetIndelHit(i) == 0)
{
continue;
}
var messyHit = _binEvidence.GetMessyHit(i);
var messyRegionHit = _binEvidence.GetMessyHit(i);
UpdateDirectionalMessStatus(directionalMessThreshold, messyRegionHit, i);
UpdateMapqMessStatus(directionalMessThreshold, i, messyRegionHit);
var isMessy = messyHit >= messySiteThreshold;
var isProbableSnv = false;
if (_collectDepth)
{
var allHitsHit = (float)_binEvidence.GetAllHits(i);
var pctMessy = messyHit / allHitsHit;
var pctIndel = _binEvidence.GetIndelHit(i) / allHitsHit;
isMessy = pctMessy + pctIndel >= imperfectFreqThreshold && pctIndel >= indelRegionFreqThreshold &&
allHitsHit >= regionDepthThreshold;
isProbableSnv = false; // TODO need to reconsider the below.
//isProbableSnv = (_singleMismatchHits[i] / (float)_allHits[i]) > 0.35;
}
if (isMessy && !isProbableSnv)
{
SetIsMessyEnoughForSiteAndNeighborsIfNotSnv(binsToExtendTo, i);
}
const int snvBinsToExtendTo = 3;
if (isProbableSnv)
{
//probableTrueSnvRegions[i] = true;
AddProbableSnvHit(i);
for (int j = 0; j < snvBinsToExtendTo; j++)
{
var binIndex = i - j;
if (!AddProbableSnvHit(binIndex))
{
break;
}
//if (binIndex >= 0)
//{
// probableTrueSnvRegions[binIndex] = true;
//}
//else
//{
// break;
//}
}
for (int j = 0; j < snvBinsToExtendTo; j++)
{
var binIndex = i + j;
if (!AddProbableSnvHit(binIndex))
{
break;
}
//if (binIndex < probableTrueSnvRegions.Length)
//{
// probableTrueSnvRegions[binIndex] = true;
//}
//else
//{
// break;
//}
}
}
}
}
