public PairwiseIBDRegion GetCopy()
{
PairwiseIBDRegion newPairwiseRegion = new PairwiseIBDRegion(this.firstIndividualID, this.secondIndividualID, this.start, this.end, this.lastBlockID, this.firstBlockID);
newPairwiseRegion.haplotype = (ArrayList)(this.haplotype).Clone();
return(newPairwiseRegion);
}
private bool CombineAdjacentPairwiseRegion(PairwiseIBDRegion firstRegion, PairwiseIBDRegion secondRegion, Individual thatIndividual)
{
if (firstRegion.GetLastBlockID() + 2 < secondRegion.GetFirstBlockID())
{
return(false);
}
else
{
int errorCount = 0;
for (int i = firstRegion.GetEnd() + 1; i < secondRegion.GetStart(); i++)
{
if (Math.Abs(this.genotype[i] - thatIndividual.genotype[i]) == 2)
{
errorCount++;
}
}
if (errorCount > 1)
{
return(false);
}
else
{
if (firstRegion.GetLastBlockID() + 2 == secondRegion.GetFirstBlockID())
{
ArrayList errorBlockHaplotypeList = new ArrayList();
foreach (HaplotypePair newPair in ((ArrayList)(this.haplotype[firstRegion.GetLastBlockID() + 1])))
{
errorBlockHaplotypeList.Add(newPair.firstHaplotypeID);
errorBlockHaplotypeList.Add(newPair.secondHaplotypeID);
}
foreach (HaplotypePair newPair in ((ArrayList)(thatIndividual.haplotype[firstRegion.GetLastBlockID() + 1])))
{
errorBlockHaplotypeList.Add(newPair.firstHaplotypeID);
errorBlockHaplotypeList.Add(newPair.secondHaplotypeID);
}
errorBlockHaplotypeList.Sort();
for (int i = 1; i < errorBlockHaplotypeList.Count; i++)
{
if (((int)(errorBlockHaplotypeList[i])) == ((int)(errorBlockHaplotypeList[i - 1])))
{
errorBlockHaplotypeList.RemoveAt(i);
i--;
}
}
firstRegion.AddHaplotype(errorBlockHaplotypeList);
}
for (int i = 0; i < secondRegion.GetHaplotypeLength(); i++)
{
firstRegion.AddHaplotype(secondRegion.GetHaplotype(i));
}
firstRegion.SetLastBlockID(secondRegion.GetLastBlockID());
firstRegion.SetEnd(secondRegion.GetEnd());
return(true); // can be combined
}
}
}
public void PairwiseComparison(ArrayList pairwiseIBDRegionList, Individual thatIndividual, Block[] blockList, MapData newMapData, double lengthCut, int startBlockID, int endBlockID)
{
PairwiseIBDRegion newPairwiseIBDRegion = new PairwiseIBDRegion(this.GetIndividualID(), thatIndividual.GetIndividualID(), 0, 0, -1, -1);
for (int blockID = startBlockID; blockID < endBlockID; blockID++) //foreach block, from first to end.
{
if (newPairwiseIBDRegion.GetLastBlockID() == -1) // last IBD region has just added or deleted, need to construc a new one.
{
newPairwiseIBDRegion.SetStart(blockList[blockID].GetStartSnpID());
newPairwiseIBDRegion.SetEnd(blockList[blockID].GetEndSnpID());
newPairwiseIBDRegion.SetLastBlockID(blockID);
newPairwiseIBDRegion.SetFirstBlockID(blockID);
newPairwiseIBDRegion.ClearHaplotype();
}
ArrayList sharedHaplotypeID = new ArrayList();
ArrayList thisHaplotypeList = new ArrayList(); //store all the possible haplotype for this individual in this block.
ArrayList thatHaplotypeList = new ArrayList(); //store all the possible haplotype for that individual in this block.
bool thisUnknownHaplotype = false;
bool thatUnknownHaplotype = false;
for (int i = 0; i < this.haplotype[blockID].Count; i++) //store all the possible haplotype for this individual in this block.
{
if (((HaplotypePair)this.haplotype[blockID][i]).firstHaplotypeID != -1)
{
thisHaplotypeList.Add(((HaplotypePair)this.haplotype[blockID][i]).firstHaplotypeID);
}
else
{
thisUnknownHaplotype = true;
break;
}
if (((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID != -1 && ((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID != ((HaplotypePair)this.haplotype[blockID][i]).firstHaplotypeID)
{
thisHaplotypeList.Add(((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID);
}
else
{
if (((HaplotypePair)this.haplotype[blockID][i]).secondHaplotypeID == -1)
{
thisUnknownHaplotype = true;
}
break;
}
}
for (int i = 0; i < thatIndividual.haplotype[blockID].Count; i++)//store all the possible haplotype for that individual in this block.
{
if (((HaplotypePair)thatIndividual.haplotype[blockID][i]).firstHaplotypeID != -1)
{
thatHaplotypeList.Add(((HaplotypePair)thatIndividual.haplotype[blockID][i]).firstHaplotypeID);
}
else
{
thatUnknownHaplotype = true;
break;
}
if (((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID != -1 && ((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID != ((HaplotypePair)thatIndividual.haplotype[blockID][i]).firstHaplotypeID)
{
thatHaplotypeList.Add(((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID);
}
else
{
if (((HaplotypePair)thatIndividual.haplotype[blockID][i]).secondHaplotypeID == -1)
{
thatUnknownHaplotype = true;
}
break;
}
}
if (thisUnknownHaplotype && thatUnknownHaplotype) //found unknown haplotype in both sample
{
for (int s = 0; s < blockList[blockID].GetHaplotypeCount(); s++)
{
sharedHaplotypeID.Add(s);
}
}
else if (thisUnknownHaplotype && !thatUnknownHaplotype) // only in this sample
{
foreach (int newId in thatHaplotypeList)
{
sharedHaplotypeID.Add(newId);
}
}
else if ((!thisUnknownHaplotype) && thatUnknownHaplotype) // only that sample
{
foreach (int newId in thisHaplotypeList)
{
sharedHaplotypeID.Add(newId);
}
}
else // normal case ,non unknown
{
thisHaplotypeList.Sort();
thatHaplotypeList.Sort();
int thisHaplotypeIndex = 0;
int thatHaplotypeIndex = 0;
while (thisHaplotypeIndex < thisHaplotypeList.Count && thatHaplotypeIndex < thatHaplotypeList.Count)
{ // store all the shared haplotype id in the sharedHaplotypeID list.
if ((int)thisHaplotypeList[thisHaplotypeIndex] == (int)thatHaplotypeList[thatHaplotypeIndex])
{
sharedHaplotypeID.Add(thisHaplotypeList[thisHaplotypeIndex]);
thisHaplotypeIndex++;
thatHaplotypeIndex++;
}
else if ((int)thisHaplotypeList[thisHaplotypeIndex] < (int)thatHaplotypeList[thatHaplotypeIndex])
{
thisHaplotypeIndex++;
}
else
{
thatHaplotypeIndex++;
}
}
}
bool shareRecombinationRegion = true;
if (sharedHaplotypeID.Count == 0) // no shared haplotype found!
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut / 10) // only add the pairwise IBD region whose length is >= 2cm
{
if (newPairwiseIBDRegion.GetLastBlockID() - newPairwiseIBDRegion.GetFirstBlockID() != 0)
{
if (pairwiseIBDRegionList.Count == 0 || !this.CombineAdjacentPairwiseRegion((PairwiseIBDRegion)pairwiseIBDRegionList[pairwiseIBDRegionList.Count - 1], newPairwiseIBDRegion, thatIndividual))
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
pairwiseIBDRegionList.Add(newPairwiseIBDRegion.GetCopy());
}
}
}
}
newPairwiseIBDRegion.SetLastBlockID(-1);
continue;
}
else
{
newPairwiseIBDRegion.SetEnd(blockList[blockID].GetEndSnpID());
newPairwiseIBDRegion.AddHaplotype(sharedHaplotypeID);
newPairwiseIBDRegion.SetLastBlockID(blockID);
if (blockID == blockList.Length - 1)
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
if (pairwiseIBDRegionList.Count == 0 || !this.CombineAdjacentPairwiseRegion((PairwiseIBDRegion)pairwiseIBDRegionList[pairwiseIBDRegionList.Count - 1], newPairwiseIBDRegion, thatIndividual))
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
pairwiseIBDRegionList.Add(newPairwiseIBDRegion.GetCopy());
}
}
}
return;
}
else
{
for (int i = blockList[blockID].GetEndSnpID() + 1; i < blockList[blockID + 1].GetStartSnpID(); i++)
{
if (Math.Abs(this.genotype[i] - thatIndividual.genotype[i]) == 2)
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut) // only add the pairwise IBD region whose length is >= 2cm
{
if (pairwiseIBDRegionList.Count == 0 || !this.CombineAdjacentPairwiseRegion((PairwiseIBDRegion)pairwiseIBDRegionList[pairwiseIBDRegionList.Count - 1], newPairwiseIBDRegion, thatIndividual))
{
if (newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetEnd()) - newMapData.GetGeneticDistance(newPairwiseIBDRegion.GetStart()) >= lengthCut)
{
pairwiseIBDRegionList.Add(newPairwiseIBDRegion.GetCopy());
}
}
}
newPairwiseIBDRegion.SetLastBlockID(-1);
newPairwiseIBDRegion.SetEnd(i - 1);
break;
}
}
}
}
}
}
public void findGroupIBD(ArrayList newIndividualList, BlockDictionary newBlockDictionary, double[,] linkageData, List <GroupShare> result, List <GroupShare> resultList, int windowStart, int windowEnd)
{
ArrayList[] IBDTable = new ArrayList[newBlockDictionary.blockList.Count];
for (int regionIndex = 0; regionIndex < pairwiseRegionList.Count; regionIndex++)//(PairwiseIBDRegion newRegion in this.pairwiseRegionList)
{
PairwiseIBDRegion newRegion = (PairwiseIBDRegion)(pairwiseRegionList[regionIndex]);
for (int blockID = newRegion.GetFirstBlockID(); blockID <= newRegion.GetLastBlockID(); blockID++)
{
foreach (int haplotypeID in newRegion.GetHaplotype(blockID - newRegion.GetFirstBlockID()))
{
if (IBDTable[blockID] == null)
{
int[] newPair = new int[2];
newPair[0] = newRegion.GetFirstIndividual();
newPair[1] = newRegion.GetSecondIndividual();
HaplotypeSharing newHaplotypeShare = new HaplotypeSharing(haplotypeID, newPair);
IBDTable[blockID] = new ArrayList();
IBDTable[blockID].Add(newHaplotypeShare);
}
else
{
bool added = false;
for (int newHaplotypeShare = 0; newHaplotypeShare < IBDTable[blockID].Count; newHaplotypeShare++)
{
if (((HaplotypeSharing)IBDTable[blockID][newHaplotypeShare]).haplotpeID == haplotypeID)
{
int[] newPair = new int[2];
newPair[0] = newRegion.GetFirstIndividual();
newPair[1] = newRegion.GetSecondIndividual();
((HaplotypeSharing)IBDTable[blockID][newHaplotypeShare]).individualList.Add(newPair);
added = true;
}
}
if (!added)
{
int[] newPair = new int[2];
newPair[0] = newRegion.GetFirstIndividual();
newPair[1] = newRegion.GetSecondIndividual();
HaplotypeSharing newHaplotypeShare = new HaplotypeSharing(haplotypeID, newPair);
IBDTable[blockID].Add(newHaplotypeShare);
}
}
}
}
pairwiseRegionList[regionIndex] = null;
}
pairwiseRegionList = null;
GC.Collect();
MyResultComparer newResultComparer = new MyResultComparer();
if (IBDTable[IBDTable.GetUpperBound(0)] == null)
{
IBDTable[IBDTable.GetUpperBound(0)] = new ArrayList();
}
for (int blockIndex = windowStart; blockIndex < windowEnd; blockIndex++)
{
ArrayList newlyComingSharingList = new ArrayList();
if (IBDTable[blockIndex] == null)
{
foreach (GroupShare newGroupShare in resultList)
{
result.Add(newGroupShare);
}
resultList = new List <GroupShare>();
IBDTable[blockIndex] = new ArrayList();
continue;
}
foreach (HaplotypeSharing newHaplotypeSharing in IBDTable[blockIndex])
{
if (newHaplotypeSharing.individualList.Count > 2 && newHaplotypeSharing.individualList.Count < 0.2 * newIndividualList.Count) //at least 2 pairs sharing this haplotype.
{
GroupShare newGroupShare = new GroupShare();
newGroupShare.sharePairList = (ArrayList)newHaplotypeSharing.individualList.Clone();
newGroupShare.allSharedFirstBlockID = blockIndex;
newGroupShare.allSharedLastBlockID = blockIndex;
newGroupShare.haplotypeList = new ArrayList();
newGroupShare.haplotypeList.Add(newHaplotypeSharing.haplotpeID);
newGroupShare.SetIndividualList();
newlyComingSharingList.Add(newGroupShare);
}
}
ArrayList newlyAddedList = new ArrayList();
//for the next block, if no haplotype contains more than 1 pair, stop the extension and record all the region waiting to be extended.
if (newlyComingSharingList.Count == 0)
{
foreach (GroupShare newGroup in resultList)
{
result.Add(newGroup);
}
}
for (int i = 0; i < resultList.Count; i++)
{
GroupShare newGroupshare1 = (GroupShare)(resultList[i]);
if (newGroupshare1.GroupShareExtention(IBDTable, newIndividualList, newBlockDictionary, newlyComingSharingList, result, newlyAddedList) == false)
{
resultList.RemoveAt(i);
i--;
}
}
foreach (GroupShare newGroupShare in newlyAddedList)
{
bool found = false;
foreach (GroupShare checkingGroup in resultList)
{
if (checkingGroup.ChekcSubGroup(newGroupShare) == true)
{
found = true;
break;
}
}
if (found == false)
{
resultList.Add(newGroupShare);
}
}
foreach (GroupShare newGroupShare in newlyComingSharingList)
{
bool found = false;
foreach (GroupShare checkingGroup in resultList)
{
if (checkingGroup.ChekcSubGroup(newGroupShare) == true)
{
found = true;
break;
}
}
if (found == false)
{
resultList.Add(newGroupShare);
}
}
resultList.Sort(newResultComparer);
}
foreach (GroupShare newShare in result)
{
newShare.SetIndividualList();
}
result.Sort(newResultComparer);
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckContain((GroupShare)(result[i + 1])) == true)
{
result.RemoveAt(i + 1);
i--;
}
else if (((GroupShare)(result[i + 1])).CheckContain(((GroupShare)(result[i]))) == true)
{
result.RemoveAt(i);
i--;
}
}
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckOverlap((GroupShare)(result[i + 1])))
{
result.RemoveAt(i + 1);
i--;
}
}
foreach (GroupShare newShare in result)
{
newShare.SetIndividualList();
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetPartiallySharedRegion(IBDTable, newBlockDictionary, newIndividualList, windowStart, windowEnd);
Console.SetCursorPosition(16, Console.CursorTop);
Console.Write("{0} / {1}", i + 1, result.Count);
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetAllSharedSnpHaplotype(newIndividualList, newBlockDictionary);
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetPartiallySharedSnpHaplotype(newIndividualList, newBlockDictionary);
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetAValue(newBlockDictionary, newIndividualList, linkageData);
}
Console.WriteLine("\t\t\t\t\tFinished.");
result.Sort(newResultComparer);
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckContain((GroupShare)(result[i + 1])))
{
result.RemoveAt(i + 1);
i--;
}
}
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckOverlap((GroupShare)(result[i + 1])))
{
result.RemoveAt(i + 1);
i--;
}
}
}
