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;
}
}
}
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 static void CheckBins(Dictionary <int, int> nonZeroBinValues, IBins <int> intBins)
{
for (int i = 0; i < 100; i++)
{
if (!nonZeroBinValues.ContainsKey(i))
{
Assert.Equal(0, intBins.GetHit(i));
}
}
foreach (var bin in nonZeroBinValues)
{
Assert.Equal(bin.Value, intBins.GetHit(bin.Key));
}
}
public void Merge(IBins <int> otherBins, int binOffset, int startBinInOther, int endBinInOther)
{
var startBinInThis = startBinInOther - binOffset;
var endBinInThis = Math.Min(_numBins, endBinInOther - binOffset);
for (int i = startBinInThis; i <= endBinInThis; i++)
{
var binIdInOtherBins = i + binOffset;
// Note, this keeps checking even if we've gone past the range of the other guy
var otherHit = otherBins.GetHit(binIdInOtherBins, false);
if (otherHit > 0)
{
IncrementHit(i, otherHit);
}
}
}
/// <summary>
/// Increment the hits of this bin with the hits from otherBins. Assumes they are on the same scale,
/// and will not go past the current bins. If offset not provided, also assumes start positions are the same.
/// </summary>
/// <param name="otherBins"></param>
/// <param name="binOffset"></param>
public void Merge(IBins <T> otherBins, int binOffset, int startBinInOther, int endBinInOther)
{
var defaultResult = ReturnDefault();
var startBinInThis = startBinInOther - binOffset;
var endBinInThis = Math.Min(_numBins, endBinInOther - binOffset);
for (int i = startBinInThis; i <= endBinInThis; i++)
{
var binIndexInOther = i + binOffset;
// Note, this keeps checking even if we've gone past the range of the other guy
var otherHit = otherBins.GetHit(binIndexInOther);
if (!otherHit.Equals(defaultResult))
{
MergeHits(i, otherHit);
}
}
}
public BinEvidence(int refId, bool collectDepth, int numBins, bool avoidLikelySnvs, int siteWidth, int regionStart, bool trackDirectionalMess = false, bool trackMapqMess = false)
{
_refId = refId;
_collectDepth = collectDepth;
NumBins = numBins;
_avoidLikelySnvs = avoidLikelySnvs;
_siteWidth = siteWidth;
_regionStart = regionStart;
// The below constants are in place to set a balance between opening up too-large groups for truly sparse data, and opening up too many small groups for globally sparse but locally dense data
// The values of the constants themselves are not really scientific and could be further honed. There is no anlaytical consequence, just performance.
const int groupSizeForCommonlyHitCategory = 500;
const int groupSizeForSparselyHitCategory = 50;
_messyHits = new SparseGroupedIntBins(NumBins, groupSizeForCommonlyHitCategory);
_indelHits = new SparseGroupedIntBins(NumBins, groupSizeForSparselyHitCategory);
if (trackDirectionalMess)
{
_fwdOnlyMessyHits = new SparseGroupedIntBins(NumBins, groupSizeForSparselyHitCategory);
_revOnlyMessyHits = new SparseGroupedIntBins(NumBins, groupSizeForSparselyHitCategory);
}
else
{
_fwdOnlyMessyHits = new DummyBins <int>();
_revOnlyMessyHits = new DummyBins <int>();
}
if (trackMapqMess)
{
_mapqMessyHits = new SparseGroupedIntBins(NumBins, groupSizeForSparselyHitCategory);
}
else
{
_mapqMessyHits = new DummyBins <int>();
}
AllHits = new DenseBins(NumBins);
_singleMismatchHits = new SparseGroupedIntBins(NumBins, groupSizeForCommonlyHitCategory);
//_singleMismatchHits = new DenseBins(NumBins); // TODO reinstate when we add single mismatch feature back
StartPosition = regionStart;
}
public void Merge(IBins <T> otherBins, int binOffset, int startBinInOther, int endBinInOther)
{
}
public void ResetIndelRegions()
{
_indelRegions = new SparseGroupedBoolBins(_binEvidence.NumBins);
}
public UsableBins(IBinConclusions binConclusions)
{
_binConclusions = binConclusions;
_numBins = binConclusions.NumBins;
_sitesUsable = new SparseGroupedBoolBins(_numBins);
}