private void AddHitForSiteAndNeighbors(int i, IBins <bool> x, int toExtendTo)
{
x.AddHit(i);
for (int j = 0; j <= toExtendTo; j++)
{
var binIndex = i - j;
if (binIndex >= 0)
{
x.AddHit(binIndex);
}
else
{
break;
}
}
for (int j = 0; j <= toExtendTo; j++)
{
var binIndex = i + j;
if (binIndex < _binEvidence.NumBins)
{
x.AddHit(binIndex);
}
else
{
break;
}
}
}
private void SetIsMessyEnoughForSiteAndNeighborsIfNotSnv(int binsToExtendTo, int i)
{
_isMessyEnough.AddHit(i);
for (int j = 0; j < binsToExtendTo; j++)
{
var binIndex = i - j;
if (binIndex >= 0)
{
if (!GetProbableTrueSnvRegion(binIndex))
{
_isMessyEnough.AddHit(binIndex);
}
}
else
{
break;
}
}
for (int j = 0; j < binsToExtendTo; j++)
{
var binIndex = i + j;
if (!GetProbableTrueSnvRegion(binIndex))
{
if (!_isMessyEnough.AddHit(binIndex))
{
break;
}
}
}
}
public void IncrementMessyHitForPosition(int i, int count)
{
var binId = (GetBinId(i));
for (int j = 0; j < count; j++)
{
_messyHits.AddHit(binId);
}
}
private void SetSiteAndNeighborsToUsable(int binsToExtendTo, int i)
{
_sitesUsable.AddHit(i);
for (int j = 0; j < binsToExtendTo; j++)
{
var binIndex = i - j;
if (binIndex >= 0)
{
if (!_binConclusions.GetProbableTrueSnvRegion(binIndex))
{
_sitesUsable.AddHit(binIndex);
}
}
else
{
break;
}
}
for (int j = 0; j < binsToExtendTo; j++)
{
var binIndex = i + j;
if (binIndex < _numBins)
{
if (!_binConclusions.GetProbableTrueSnvRegion(binIndex))
{
_sitesUsable.AddHit(binIndex);
}
}
else
{
break;
}
}
}
private void AddSingleMismatchHit(int i)
{
_singleMismatchHits.AddHit(i);
}
public void AddMessEvidence(bool isMessy, PairResult pairResult, bool isIndel, bool isSingleMismatch, bool isForwardOnlyMessy, bool isReverseOnlyMessy, bool isMapqMessy)
{
if (!_collectDepth && !isMessy && !isIndel && !isForwardOnlyMessy && !isMapqMessy && !isReverseOnlyMessy && !isSingleMismatch)
{
return;
}
foreach (var aln in pairResult.Alignments)
{
if (aln.RefID != _refId)
{
continue;
}
var lastBinSpannedByRead = GetBinId(aln.EndPosition);
var firstBin = GetBinId(aln.Position);
if (lastBinSpannedByRead + 1 > NumBins - 1)
{
Console.WriteLine("LAST BIN SPANNED IS GREATER THAN ALLHITS!!!");
}
for (int i = firstBin; i <= Math.Min(lastBinSpannedByRead, NumBins - 1); i++)
{
try
{
AllHits.AddHit(i);
if (isMessy)
{
AddMessyHit(i);
if (isForwardOnlyMessy)
{
_fwdOnlyMessyHits.AddHit(i);
}
else if (isReverseOnlyMessy)
{
_revOnlyMessyHits.AddHit(i);
}
else if (isMapqMessy)
{
_mapqMessyHits.AddHit(i);
}
}
if (isIndel)
{
AddIndelHit(i);
}
if (isSingleMismatch)
{
AddSingleMismatchHit(i);
}
}
catch (Exception e)
{
Console.WriteLine($"FAILED ON {i} ({aln.Position}, {_regionStart})..." + e.Message);
throw new Exception($"FAILED ON {i} ({aln.Position}, {_regionStart})", e);
}
}
}
}
private bool AddProbableSnvHit(int i)
{
return(_probableTrueSnvRegions.AddHit(i));
}
public bool SetIndelRegionTrue(int i)
{
return(_indelRegions.AddHit(i));
}
