public void PrintResult(BlockDictionary newBlockDictionary, int totalCase, double maxIndRate, Commands newCommands)
{
MyResultAValueComparer newComparer = new MyResultAValueComparer();
result.Sort(newComparer);
FileStream cFile = new FileStream(newCommands.outputName, FileMode.Append);
StreamWriter sw1 = new StreamWriter(cFile);
if (result.Count == 0)
{
return;
}
int count = 0;
for (int i = 0; i < result.Count; i++)
{
if (i > 200 && (((GroupShare)result[i]).AValue > 0.05 || ((GroupShare)result[i]).individualList.Count > totalCase * maxIndRate))
{
//limit++;
continue;
}
Block firstBlock = ((Block)(newBlockDictionary.blockList[((GroupShare)result[i]).allSharedFirstBlockID]));
Block lastBlock = ((Block)(newBlockDictionary.blockList[((GroupShare)result[i]).allSharedLastBlockID]));
double a = 1.0 / ((GroupShare)result[i]).AValue;
sw1.Write("{0}\t", ((GroupShare)result[i]).AValue);
sw1.Write("{0}\t{1}\t{2:00000.0}\t{3}:{4}\t{5}\t", newCommands.chromosome, ((GroupShare)result[i]).individualList.Count, (lastBlock.GetEnd() - firstBlock.GetStart()) / 1000, firstBlock.GetStart(), lastBlock.GetEnd(), lastBlock.GetEndSnpID() - firstBlock.GetStartSnpID() + 1);
for (int j = 0; j < ((GroupShare)result[i]).individualList.Count; j++)
{
if (j < ((GroupShare)result[i]).individualList.Count - 1)
{
sw1.Write("{0},", ((GroupShare)result[i]).individualList[j]);
}
else
{
sw1.Write("{0}\t", ((GroupShare)result[i]).individualList[j]);
}
}
sw1.Write("{0}:{1}\t", firstBlock.GetStartSnpID(), lastBlock.GetEndSnpID());
for (int j = 0; j < ((GroupShare)result[i]).individualList.Count; j++)
{
if (j < ((GroupShare)result[i]).individualList.Count - 1)
{
sw1.Write("{0}:{1},", (((Block)(newBlockDictionary.blockList[((GroupShare)result[i]).partiallySharedRegion[j, 0]])).GetStartSnpID()), (((Block)(newBlockDictionary.blockList[((GroupShare)result[i]).partiallySharedRegion[j, 1]])).GetEndSnpID()));
}
else
{
sw1.Write("{0}:{1}\t", (((Block)(newBlockDictionary.blockList[((GroupShare)result[i]).partiallySharedRegion[j, 0]])).GetStartSnpID()), (((Block)(newBlockDictionary.blockList[((GroupShare)result[i]).partiallySharedRegion[j, 1]])).GetEndSnpID()));
}
}
for (int blockID = ((GroupShare)result[i]).allSharedFirstBlockID; blockID <= ((GroupShare)result[i]).allSharedLastBlockID; blockID++)
{
Block currentBlock = ((Block)(newBlockDictionary.blockList[blockID]));
sw1.Write("|");
for (int snpID = 0; snpID <= currentBlock.GetEndSnpID() - currentBlock.GetStartSnpID(); snpID++)
{
sw1.Write("{0}", currentBlock.Gethaplotype((int)(((GroupShare)result[i]).haplotypeList[blockID - ((GroupShare)result[i]).allSharedFirstBlockID]), snpID));
}
if (blockID == ((GroupShare)result[i]).allSharedLastBlockID)
{
break;
}
sw1.Write("|");
for (int snpID = currentBlock.GetEndSnpID() + 1; snpID < ((Block)(newBlockDictionary.blockList[blockID + 1])).GetStartSnpID(); snpID++)
{
sw1.Write("-");
}
}
sw1.Write("\t");
for (int blockID = ((GroupShare)result[i]).allSharedFirstBlockID; blockID <= ((GroupShare)result[i]).allSharedLastBlockID; blockID++)
{
sw1.Write("{0},", ((Block)(newBlockDictionary.blockList[blockID])).GetFrequency((int)(((GroupShare)result[i]).haplotypeList[blockID - ((GroupShare)result[i]).allSharedFirstBlockID])).ToString("0.0000"));
}
sw1.WriteLine();
if (i > 4)
{
count++;
}
}
Console.Write("{0} regions found in cases, {1} regions found to be with significant p value (0.05).\nFinished writing significant results in outputfile.", this.result.Count, count);
sw1.Close();
}
public void SetAValue(BlockDictionary newBlockDictionary, ArrayList newIndividualList, double[,] newLinkageData)
{
double[] singleP = new double[this.individualList.Count];
for (int i = 0; i < this.individualList.Count; i++)
{
for (int j = this.partiallySharedRegion[i, 0]; j <= this.partiallySharedRegion[i, 1] && j <= this.partiallySharedLastBlockID; j++)
{
double nextFrequency = ((Block)(newBlockDictionary.blockList[j])).GetFrequency((int)(this.partiallySharedBlockHaplotype[j - this.partiallySharedFirstBlockID]));
nextFrequency = 0.0 - Math.Log10(nextFrequency);
singleP[i] += nextFrequency;
if (j != this.partiallySharedRegion[i, 1] && j != this.partiallySharedLastBlockID)
{
ArrayList recombinationSnpList = new ArrayList();
for (int k = ((Block)(newBlockDictionary.blockList[j])).GetEndSnpID() - ((Block)(newBlockDictionary.blockList[this.partiallySharedFirstBlockID])).GetStartSnpID() + 1; k <= ((Block)(newBlockDictionary.blockList[j + 1])).GetStartSnpID() - ((Block)(newBlockDictionary.blockList[this.partiallySharedFirstBlockID])).GetStartSnpID() - 1; k++)
{
recombinationSnpList.Add(this.partiallySharedSnpHaplotype[k]);
}
nextFrequency = Math.Log10(this.GetRecombinationAValue(((Block)(newBlockDictionary.blockList[j])).GetEndSnpID() + 1, recombinationSnpList, newLinkageData));
}
}
}
for (int i = 0; i < this.individualList.Count; i++)
{
this.AValue += singleP[i];
if (i == 10)
{
break;
}
}
double sharedRegionAValue = 0;
for (int i = allSharedFirstBlockID; i <= allSharedLastBlockID; i++)
{
sharedRegionAValue -= Math.Log10(((Block)(newBlockDictionary.blockList[i])).GetFrequency((int)haplotypeList[i - allSharedFirstBlockID]));
if (i != allSharedLastBlockID)
{
ArrayList recombinationSnpList = new ArrayList();
for (int j = ((Block)(newBlockDictionary.blockList[i])).GetEndSnpID() - ((Block)(newBlockDictionary.blockList[this.allSharedFirstBlockID])).GetStartSnpID() + 1; j <= ((Block)(newBlockDictionary.blockList[i + 1])).GetStartSnpID() - ((Block)(newBlockDictionary.blockList[this.allSharedFirstBlockID])).GetStartSnpID() - 1; j++)
{
recombinationSnpList.Add(this.allSharedSnpHaplotype[j]);
}
if (sharedRegionAValue > 1000000)
{
Console.Write("here");
}
}
if (i == 10)
{
break;
}
}
double h0 = 1;
for (int newBlockIndex = this.partiallySharedFirstBlockID; newBlockIndex <= this.partiallySharedLastBlockID; newBlockIndex++)
{
int shareCount = 0;
for (int i = 0; i < this.individualList.Count; i++)
{
if (this.partiallySharedRegion[i, 0] <= newBlockIndex && this.partiallySharedRegion[i, 1] >= newBlockIndex)
{
shareCount++;
}
}
h0 += Math.Log10(Math.Pow(2, shareCount)) - CombinationLog(shareCount, shareCount * 2);
}
h0 = h0 - this.AValue;
int generation;
double length;
length = (((Block)(newBlockDictionary.blockList[this.partiallySharedLastBlockID])).GetEnd() - ((Block)(newBlockDictionary.blockList[this.partiallySharedFirstBlockID])).GetStart()) / 1000000.0;
generation = Convert.ToInt32(1.0 / length * 100);
double h1 = Math.Log10(0.5) * this.individualList.Count * generation;
this.AValue = h1 - h0;
}
static void Main(string[] args)
{
Commands newCommends = new Commands();
if (!newCommends.ReadCommand(args))
{
return;
}
Stopwatch stw = new Stopwatch();
stw.Start();
if (newCommends.chromosome == 0)
{
Regex r = new Regex(@"[0-9]+");
FileStream cFile = new FileStream(newCommends.outputName, FileMode.Create);
cFile.Close();
for (int i = 1; i < 23; i++)
{
//Console.WriteLine(i);
newCommends.chromosome = i;
newCommends.pedName = r.Replace(newCommends.pedName, i.ToString());
newCommends.mapName = r.Replace(newCommends.mapName, i.ToString());
//newCommends.
Console.WriteLine("Start reading file data:");
Console.Write("\tReading genetic distance data...");
GeneticDistance geneticdistance = new GeneticDistance(); //store all the snp genetic distance and recombination data.
geneticdistance.InitialGeniticDistance(0, 300000, newCommends);
Console.Write("finished.\n");
Console.Write("\tReading map data...");
MapData mapdata = new MapData(); //store all the snp physical position in the map file.
mapdata.ReadMapFile(newCommends);
mapdata.ReadGeneticDistance(geneticdistance);
Console.Write("finished.\n");
Console.Write("\tReading haplotype frequency data...");
BlockDictionary newDictionary = new BlockDictionary(newCommends); //store all the block haplotype information in the Dictionary, the object type is Block.
newDictionary.Localization(mapdata);
Console.Write("finished.\n");
Main newEvaluation = new Main();
newEvaluation.Evalation(geneticdistance, mapdata, newDictionary, newCommends);
}
return;
}
else
{
FileStream cFile = new FileStream(newCommends.outputName, FileMode.Create);
cFile.Close();
Console.WriteLine("Start reading file data:");
Console.Write("\tReading genetic distance data...");
GeneticDistance geneticdistance = new GeneticDistance(); //store all the snp genetic distance and recombination data.
geneticdistance.InitialGeniticDistance(0, 300000, newCommends);
Console.Write("finished.\n");
Console.Write("\tReading map data...");
MapData mapdata = new MapData(); //store all the snp physical position in the map file.
mapdata.ReadMapFile(newCommends);
mapdata.ReadGeneticDistance(geneticdistance);
Console.Write("finished.\n");
Console.Write("\tReading haplotype frequency data...");
BlockDictionary newDictionary = new BlockDictionary(newCommends); //store all the block haplotype information in the Dictionary, the object type is Block.
newDictionary.Localization(mapdata);
Console.Write("finished.\n");
Main newEvaluation = new Main();
newEvaluation.Evalation(geneticdistance, mapdata, newDictionary, newCommends);
return;
}
stw.Stop();
}
public void SetPartiallySharedRegion(ArrayList[] IBDTable, BlockDictionary newBlockDictionary, ArrayList wholeIndividualList, int windowStart, int windowEnd)
{
this.partiallySharedRegion = new int[this.individualList.Count, 2];
this.partiallySharedBlockHaplotype = new ArrayList();
this.partiallySharedFirstBlockID = windowStart;
this.partiallySharedLastBlockID = windowEnd - 1;
//set the start point of the partially shared region.
ArrayList lastRemainingIndividual = (ArrayList)this.individualList.Clone();
for (int blockID = allSharedFirstBlockID - 1; blockID >= windowStart; blockID--)
{
int bestSharedHaplotype = -1;
ArrayList remainningIndividual = new ArrayList();
foreach (HaplotypeSharing newHaplotypeSharing in IBDTable[blockID]) //find the best sharing haplotype in this block.
{
ArrayList intersection = this.SimpleIntersection(lastRemainingIndividual, newHaplotypeSharing.individualList);
if (intersection.Count > remainningIndividual.Count)
{
remainningIndividual = (ArrayList)intersection.Clone();
bestSharedHaplotype = newHaplotypeSharing.haplotpeID;
if (remainningIndividual.Count == lastRemainingIndividual.Count)
{
//if (remainningIndividual.Count == this.individualList.Count)
//this.allSharedFirstBlockID = blockID;
break;
}
}
}
/*
* for (int recombinationSnpIndex = ((Block)(newBlockDictionary.blockList[blockID + 1])).GetStartSnpID() - 1; recombinationSnpIndex > ((Block)(newBlockDictionary.blockList[blockID])).GetEndSnpID(); recombinationSnpIndex--)
* {
* ArrayList commonAlleleList = new ArrayList();
* ArrayList rareAlleleList = new ArrayList();
* for (int remainingIndex = 0; remainingIndex < remainningIndividual.Count; remainingIndex++)
* {
* if (((Individual)(wholeIndividualList[(int)remainningIndividual[remainingIndex]])).genotype[recombinationSnpIndex] == 0)
* rareAlleleList.Add(remainingIndex);
* else if (((Individual)(wholeIndividualList[(int)remainningIndividual[remainingIndex]])).genotype[recombinationSnpIndex] == 2)
* commonAlleleList.Add(remainingIndex);
* ArrayList removeList = new ArrayList();
* if (rareAlleleList.Count >= commonAlleleList.Count)
* removeList = (ArrayList)commonAlleleList.Clone();
* else
* removeList = (ArrayList)rareAlleleList.Clone();
* removeList.Sort();
* removeList.Reverse();
* for (int removeIndex = 0; removeIndex < removeList.Count; removeIndex++)
* remainningIndividual.RemoveAt((int)removeList[removeIndex]);
* }
* }
*/
if (remainningIndividual.Count > 1)
{
partiallySharedBlockHaplotype.Insert(0, bestSharedHaplotype);
if (remainningIndividual.Count == lastRemainingIndividual.Count)
{
continue;
}
else
{
ArrayList difference = this.GetDifferenceSet(lastRemainingIndividual, remainningIndividual);
foreach (int i in difference)
{
this.partiallySharedRegion[this.GetIndividualOrderInList(i), 0] = blockID + 1;
}
lastRemainingIndividual = (ArrayList)remainningIndividual.Clone();
}
}
else
{
foreach (int i in lastRemainingIndividual)
{
this.partiallySharedRegion[this.GetIndividualOrderInList(i), 0] = blockID + 1;
}
this.partiallySharedFirstBlockID = blockID + 1;
//this.firstBlockID = blockID + 1;
break;
}
}
for (int i = 0; i < this.individualList.Count; i++)
{
if (partiallySharedRegion[i, 0] == 0)
{
partiallySharedRegion[i, 0] = windowStart;
}
}
for (int i = 0; i < this.haplotypeList.Count; i++)
{
partiallySharedBlockHaplotype.Add(this.haplotypeList[i]);
}
//set the end point of the partially shared region.
lastRemainingIndividual = (ArrayList)this.individualList.Clone();
for (int blockID = allSharedLastBlockID + 1; blockID < windowEnd; blockID++)
{
int bestSharedHaplotype = -1;
ArrayList remainningIndividual = new ArrayList();
foreach (HaplotypeSharing newHaplotypeSharing in IBDTable[blockID]) //find the best sharing haplotype in this block.
{
ArrayList intersection = this.SimpleIntersection(lastRemainingIndividual, newHaplotypeSharing.individualList);
if (intersection.Count > remainningIndividual.Count)
{
remainningIndividual = (ArrayList)intersection.Clone();
bestSharedHaplotype = newHaplotypeSharing.haplotpeID;
if (remainningIndividual.Count == lastRemainingIndividual.Count)
{
//if (remainningIndividual.Count == this.individualList.Count)
//this.allSharedLastBlockID = blockID;
break;
}
}
}
if (remainningIndividual.Count > 1)
{
partiallySharedBlockHaplotype.Add(bestSharedHaplotype);
if (remainningIndividual.Count == lastRemainingIndividual.Count)
{
continue;
}
else
{
ArrayList difference = this.GetDifferenceSet(lastRemainingIndividual, remainningIndividual);
foreach (int i in difference)
{
this.partiallySharedRegion[this.GetIndividualOrderInList(i), 1] = blockID - 1;
}
lastRemainingIndividual = (ArrayList)remainningIndividual.Clone();
}
}
else
{
foreach (int i in lastRemainingIndividual)
{
this.partiallySharedRegion[this.GetIndividualOrderInList(i), 1] = blockID - 1;
}
this.partiallySharedLastBlockID = blockID - 1;
//this.lastBlockID = blockID - 1;
break;
}
}
for (int i = 0; i < this.individualList.Count; i++)
{
if (partiallySharedRegion[i, 1] == 0)
{
partiallySharedRegion[i, 1] = windowEnd;
}
}
/*
* int remainIndividual = 0;
* for (int i = 0; i < this.individualList.Count; i++)
* {
* if (((Block)(newBlockDictionary.blockList[partiallySharedRegion[i, 1]])).GetEndSnpID() - ((Block)(newBlockDictionary.blockList[partiallySharedRegion[i, 0]])).GetStartSnpID() <= 10)
* {
* this.partiallySharedRegion[i, 0] = -1;
* this.partiallySharedRegion[i, 1] = -1;
* }
* else
* remainIndividual++;
* }
* ArrayList newIndividualList = new ArrayList();
* int[,] newPartiallySharedRegion = new int[remainIndividual, 2];
* int individualOrder = 0;
* for (int i = 0; i < this.individualList.Count; i++)
* {
* if (this.partiallySharedRegion[i, 0] >= 0)
* {
* newIndividualList.Add(this.individualList[i]);
* newPartiallySharedRegion[individualOrder, 0] = this.partiallySharedRegion[i, 0];
* newPartiallySharedRegion[individualOrder, 1] = this.partiallySharedRegion[i, 1];
* individualOrder++;
* }
* }
* this.individualList = (ArrayList)(newIndividualList.Clone());
* this.partiallySharedRegion = (int[,])newPartiallySharedRegion.Clone();
*/
if (this.individualList.Count < 2)
{
return;
}
while (this.allSharedFirstBlockID > windowStart)
{
bool foundUpperBound = false;
for (int i = 0; i < this.individualList.Count; i++)
{
if (this.partiallySharedRegion[i, 0] >= this.allSharedFirstBlockID)
{
foundUpperBound = true;
break;
}
}
if (foundUpperBound)
{
break;
}
else
{
this.allSharedFirstBlockID--;
this.haplotypeList.Insert(0, this.partiallySharedBlockHaplotype[this.allSharedFirstBlockID - this.partiallySharedFirstBlockID]);
//break;
}
}
while (this.allSharedLastBlockID < this.partiallySharedLastBlockID)
{
bool foundLowerBound = false;
for (int i = 0; i < this.individualList.Count; i++)
{
if (this.partiallySharedRegion[i, 1] <= this.allSharedLastBlockID)
{
foundLowerBound = true;
break;
}
}
if (foundLowerBound)
{
break;
}
else
{
// if (this.allSharedLastBlockID >= windowEnd)
// break;
this.allSharedLastBlockID++;
this.haplotypeList.Add(this.partiallySharedBlockHaplotype[this.allSharedLastBlockID - this.partiallySharedFirstBlockID]);
}
}
if (this.partiallySharedLastBlockID == 0)
{
this.partiallySharedLastBlockID = this.allSharedLastBlockID;
}
}
public bool GroupShareExtention(ArrayList[] IBDTable, ArrayList newIndividualList, BlockDictionary newBlockDictionary, ArrayList newlyComingSharingList, List <GroupShare> finalResultList, ArrayList newlyAddedList)
{
if (this.allSharedLastBlockID >= IBDTable.GetUpperBound(0)) //the end of the block list, add to result if still some sharing left
{
if (this.individualList.Count > 1 && (this.allSharedLastBlockID - this.allSharedFirstBlockID >= 2)) //add to result list
{
finalResultList.Add((GroupShare)this.MemberwiseClone());
}
}
bool foundNext = false; //if find haplotype that can continue all the individuals in the next block, then "this" will not be added to list
ArrayList passList = new ArrayList();
ArrayList waitingToAddGroupList = new ArrayList();
for (int haplotypeIndex = 0; haplotypeIndex < newlyComingSharingList.Count; haplotypeIndex++)
{
bool foundBefore = false;
ArrayList pairListIntersection;
pairListIntersection = this.GetPairListIntersection(this.sharePairList, ((GroupShare)(newlyComingSharingList[haplotypeIndex])).sharePairList);
if (pairListIntersection.Count == this.sharePairList.Count)
{
foundNext = true;
this.allSharedLastBlockID += 1;
this.haplotypeList.Add(((GroupShare)(newlyComingSharingList[haplotypeIndex])).haplotypeList[0]);
if (pairListIntersection.Count == ((GroupShare)(newlyComingSharingList[haplotypeIndex])).sharePairList.Count)
{
newlyComingSharingList.RemoveAt(haplotypeIndex);
haplotypeIndex--;
}
return(true);
}
foreach (ArrayList eachList in passList) //check this intersection has already go checking next block, so do not need to do again for this subgroup.
{
if (eachList.Count != pairListIntersection.Count)
{
continue;
}
else
{
for (int i = 0; i < pairListIntersection.Count; i++)
{
if (((int[])pairListIntersection[i])[0] != ((int[])(eachList[i]))[0] || ((int[])pairListIntersection[i])[1] != ((int[])(eachList[i]))[1])
{
break;
}
if (i == (pairListIntersection.Count - 1) && ((int[])pairListIntersection[i])[0] == ((int[])(eachList[i]))[0] && ((int[])pairListIntersection[i])[1] == ((int[])(eachList[i]))[1])
{
foundBefore = true;
}
}
}
}
if (foundBefore == true) //checked before, do not need to go checking
{
break;
}
if (pairListIntersection.Count > 1)
{
passList.Add(pairListIntersection.Clone());
GroupShare newGroupShare = new GroupShare();
newGroupShare.sharePairList = (ArrayList)pairListIntersection.Clone();
newGroupShare.allSharedLastBlockID = this.allSharedLastBlockID + 1;
newGroupShare.allSharedFirstBlockID = this.allSharedFirstBlockID;
newGroupShare.haplotypeList = (ArrayList)this.haplotypeList.Clone();
newGroupShare.haplotypeList.Add(((GroupShare)(newlyComingSharingList[haplotypeIndex])).haplotypeList[0]);
newGroupShare.SetIndividualList();
if (newGroupShare.CheckRecombinationRegion(newIndividualList, newBlockDictionary)) // need to check the recombination region first.
{
waitingToAddGroupList.Add(newGroupShare);
}
}
if (foundNext == false && (this.allSharedLastBlockID - this.allSharedFirstBlockID >= 2))
{
finalResultList.Add((GroupShare)(this.MemberwiseClone()));
}
}
MyPrivateResultComparer newPrivateResultComparer = new MyPrivateResultComparer();
waitingToAddGroupList.Sort(newPrivateResultComparer);
for (int i = 0; i < waitingToAddGroupList.Count - 1; i++)
{
for (int j = i + 1; j < waitingToAddGroupList.Count; j++)
{
if (((GroupShare)(waitingToAddGroupList[i])).ChekcSubGroup(((GroupShare)(waitingToAddGroupList[j]))) == true)
{
waitingToAddGroupList.RemoveAt(j);
j--;
}
}
}
foreach (GroupShare newGroupShare in waitingToAddGroupList)
{
if (newlyAddedList.Count == 0)
{
newlyAddedList.Add(newGroupShare);
}
else
{
for (int i = 0; i < newlyAddedList.Count; i++)
{
if (((GroupShare)(newlyAddedList[i])).ChekcSubGroup(newGroupShare) == true)
{
break;
}
if (newGroupShare.ChekcSubGroup((GroupShare)(newlyAddedList[i])) == true)
{
newlyAddedList[i] = newGroupShare;
break;
}
if (i == newlyAddedList.Count - 1)
{
newlyAddedList.Add(newGroupShare);
}
}
}
}
return(false);
}
public void PerformeSimulation(int populationSize, GeneticDistance geneticDistance, MapData mapData, ArrayList individualList, BlockDictionary blockDictionary, double[,] caseLinkageData) //random choose offspringID, simulat all offspring
{
inheritPosition = new int[this.offsprings.Length, 2];
Random randomSeed = new Random();
this.ancenstor = randomSeed.Next(populationSize);
for (int i = 0; i < this.offsprings.Length; i++) //sumulate every offspring id.
{
int newOffspring = new int();
newOffspring = randomSeed.Next(populationSize);
bool found = false;
for (int j = 0; j < i; j++) //simulate offspring id, random choose from population
{
if (this.offsprings[j] == newOffspring || newOffspring == this.ancenstor) //avoid same id.
{
i--;
found = true;
break;
}
}
if (found)
{
continue;
}
else
{
this.SetOffspring(i, newOffspring);
this.SingleSimulation(i, geneticDistance, mapData);
if (this.inheritPosition[i, 0] == 0 && this.inheritPosition[i, 1] == 0)
{
i--;
}
}
}
this.SetSimulatedData(individualList, blockDictionary, mapData, caseLinkageData);
//Console.ReadKey();
}
private void SetSimulatedData(ArrayList individualList, BlockDictionary blockDictionary, MapData mapData, double[,] caseLinkageData) // haplotype the ancestor's genotype data, substitude one haplotype for each simulated offspring.
{
int[] ancenstorHaplotype1 = new int[((Individual)individualList[this.ancenstor]).genotype.Length];
int[] ancenstorHaplotype2 = new int[((Individual)individualList[this.ancenstor]).genotype.Length];
FileStream cFile = new FileStream(@"simulation.txt", FileMode.Create);
StreamWriter sw1 = new StreamWriter(cFile);
for (int simulationIndex = 0; simulationIndex < this.offsprings.Length + 1; simulationIndex++) //haplotyping for the ancenstor and the offspings.
{
int haplotypingIndex;
if (simulationIndex == 0)
{
haplotypingIndex = this.ancenstor;
}
else
{
haplotypingIndex = this.offsprings[simulationIndex - 1];
}
((Individual)individualList[haplotypingIndex]).haplotype = new ArrayList[blockDictionary.blockList.Count];
int blockID = -1;
foreach (Block newBlock in blockDictionary.blockList)
{
blockID++;
if (newBlock.GetEndSnpID() + newBlock.GetStartSnpID() == 0)
{
continue;
}
int[] blockGenotype = new int[newBlock.GetEndSnpID() - newBlock.GetStartSnpID() + 1];
for (int snpID = newBlock.GetStartSnpID(); snpID <= newBlock.GetEndSnpID(); snpID++)
{
blockGenotype[snpID - newBlock.GetStartSnpID()] = ((Individual)individualList[haplotypingIndex]).genotype[snpID];
}
ArrayList newHaplotypePairList = newBlock.GenotypeToHaplotype(blockGenotype, caseLinkageData);
((Individual)individualList[haplotypingIndex]).haplotype[blockID] = newHaplotypePairList;
}
//Haplotyping for the ancenstor.
int[] haplotype1 = new int[((Individual)individualList[haplotypingIndex]).genotype.Length];
int[] haplotype2 = new int[((Individual)individualList[haplotypingIndex]).genotype.Length];
blockID = 0;
Random randomseed = new Random();
for (int snpIndex = 0; snpIndex < ((Individual)individualList[haplotypingIndex]).genotype.Length; snpIndex++)
{
if (blockID >= blockDictionary.blockList.Count || mapData.physicalDistance[snpIndex] < ((Block)blockDictionary.blockList[blockID]).GetStart()) // this snp is not in the current block.
{
if (snpIndex == 0) // start of the simulated region.
{
haplotype1[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] / 2;
haplotype1[snpIndex] = (((Individual)individualList[haplotypingIndex]).genotype[snpIndex] + 1) / 2;
}
else
{
if (((Individual)individualList[haplotypingIndex]).genotype[snpIndex] == 0) //two major
{
haplotype1[snpIndex] = 0;
haplotype2[snpIndex] = 0;
}
else if (((Individual)individualList[haplotypingIndex]).genotype[snpIndex] == 2) //two minor
{
haplotype1[snpIndex] = 1;
haplotype2[snpIndex] = 1;
}
else // major + minor combination at that snp.
{
if (haplotype1[snpIndex - 1] == haplotype2[snpIndex - 1]) //if the last snp is not the major+minor combination
{
if (randomseed.NextDouble() <= 0.5)
{
haplotype1[snpIndex] = 0;
haplotype2[snpIndex] = 1;
}
else
{
haplotype1[snpIndex] = 1;
haplotype2[snpIndex] = 0;
}
}
else
{
if (randomseed.NextDouble() <= caseLinkageData[snpIndex - 1, 6])
{
haplotype1[snpIndex] = haplotype1[snpIndex - 1];
haplotype2[snpIndex] = haplotype2[snpIndex - 1];
}
else
{
haplotype1[snpIndex] = haplotype2[snpIndex - 1];
haplotype2[snpIndex] = haplotype1[snpIndex - 1];
}
}
}
}
}
else //the snp is in or after the current block
{
if (mapData.physicalDistance[snpIndex] > ((Block)blockDictionary.blockList[blockID]).GetEnd()) //after the current block.
{
blockID++;
snpIndex--;
}
else //in the current block
{
// the two haplotype in the block is with the same start allele or the last snp is not major+minor.
if (((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).secondHaplotypeID == -1)
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype1[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype2[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype1[snpIndex];
}
snpIndex--;
}
else
{
if (snpIndex == 0 || ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] != 1 || ((Individual)individualList[haplotypingIndex]).genotype[snpIndex - 1] != 1)// the two haplotype in the block is with the same start allele or the last snp is not major+minor.
{
if (randomseed.NextDouble() <= 0.5)
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype1[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype2[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype1[snpIndex];
}
}
else
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype2[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype1[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype2[snpIndex];
}
}
snpIndex--;
}
else // 1 + 1 major+minor before major + minor in block.
{
if (randomseed.NextDouble() <= caseLinkageData[snpIndex - 1, 6]) //AaBb -> AB+ab
{
if (haplotype1[snpIndex - 1] == ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, 0))
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype1[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype2[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype1[snpIndex];
}
snpIndex--;
}
else
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype2[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype1[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype2[snpIndex];
}
snpIndex--;
}
}
else //AaBb -> Ab+aB
{
if (haplotype1[snpIndex - 1] == ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, 0))
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype2[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype1[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype2[snpIndex];
}
snpIndex--;
}
else
{
for (snpIndex = ((Block)blockDictionary.blockList[blockID]).GetStartSnpID(); snpIndex <= ((Block)blockDictionary.blockList[blockID]).GetEndSnpID(); snpIndex++)
{
haplotype1[snpIndex] = ((Block)blockDictionary.blockList[blockID]).Gethaplotype(((HaplotypePair)((Individual)individualList[haplotypingIndex]).haplotype[blockID][0]).firstHaplotypeID, snpIndex - ((Block)blockDictionary.blockList[blockID]).GetStartSnpID());
haplotype2[snpIndex] = ((Individual)individualList[haplotypingIndex]).genotype[snpIndex] - haplotype1[snpIndex];
}
snpIndex--;
}
}
}
}
}
}
}
if (simulationIndex == 0)
{
ancenstorHaplotype1 = (int[])haplotype1.Clone();
ancenstorHaplotype2 = (int[])haplotype2.Clone();
}
else
{
for (int m = this.inheritPosition[simulationIndex - 1, 0]; m <= this.inheritPosition[simulationIndex - 1, 1]; m++)
{
haplotype2[m] = ancenstorHaplotype1[m];
((Individual)individualList[haplotypingIndex]).genotype[m] = haplotype1[m] + haplotype2[m];
}
}
if (simulationIndex == 0)
{
sw1.Write("{0}\t{1} to {2}\t", haplotypingIndex, 0, 3569);
}
else
{
sw1.Write("{0}\t{1} to {2}\t", haplotypingIndex, this.inheritPosition[simulationIndex - 1, 0], this.inheritPosition[simulationIndex - 1, 1]);
}
for (int i = 0; i < ((Individual)individualList[haplotypingIndex]).genotype.Length; i++)
{
if (simulationIndex == 0 || i >= this.inheritPosition[simulationIndex - 1, 0] && i <= this.inheritPosition[simulationIndex - 1, 1])
{
sw1.Write("{0}", ((Individual)individualList[haplotypingIndex]).genotype[i]);
}
else
{
sw1.Write("-");
}
}
sw1.WriteLine();
sw1.WriteLine();
}
sw1.Close();
}
public void CaseControlEvaluation(GeneticDistance newGeneticDistance, MapData newMapData, BlockDictionary newBlockDictionary, Commands newCommands, ResultList finalResultList)
{
SnpDataSet caseData = new SnpDataSet(); //Creat Case data set
SnpDataSet controlData = new SnpDataSet(); //Creat Control data set
Console.Write("\tReading ped data...");
Inputdata inputData = new Inputdata();
inputData.data(caseData, controlData, newCommands); //start getting the data and put into case/comtrol set
ArrayList controlIndividualList = new ArrayList();
ArrayList caseIndividualList = new ArrayList();
Console.Write("finished.\n");
inputData = null;
GC.Collect();
Console.Write("Analyzing LD data...");
double[,] controlLinkageData = new double[controlData.GetSnpCount(), 7];
//caseData.Linkage(caseLinkageData);
controlData.SetIndividualList(controlIndividualList);
controlData = null;
GC.Collect();
Console.Write("finished.\n");
finalResultList.SetControlResult(caseData.individual.Length, 0.2);
Console.WriteLine("Haplotyping for all the control samples...");
for (int indIndex = 0; indIndex < controlIndividualList.Count; indIndex++)
{
((Individual)(controlIndividualList[indIndex])).SetIndividualID(indIndex);
}
int ind = 0;
foreach (Individual newIndividual in controlIndividualList) //haplotyping for each individual.
{
newIndividual.Haplotyping(newBlockDictionary, newMapData, controlLinkageData);
ind++;
Console.SetCursorPosition(8, Console.CursorTop);
Console.Write("{0} / {1}", ind, controlIndividualList.Count);
}
Console.Write("\t\tFinished.\n");
for (int n = 0; n < newCommands.permutation; n++) //permutation
{
Console.Write("Iteration: {0} / {1} \n", n + 1, newCommands.permutation);
List <GroupShare> resultList = new List <GroupShare>(); //unfinished result from last window
List <int> selectControlList = new List <int>();
selectControlList = this.Select(controlIndividualList.Count, caseData.individual.Length, new Random());
//selectControlList = this.Select(controlIndividualList.Count, 30, new Random());
for (int windowStart = 0; windowStart <= newBlockDictionary.blockList.Count - 1; windowStart += 30000)
{
List <GroupShare> newResultList = new List <GroupShare>();
int windowEnd = Math.Min(windowStart + 30000, newBlockDictionary.blockList.Count - 1);
ArrayList wholePairwiseIBDRegionList = new ArrayList();
Console.WriteLine("\t\tSearching for pairwise sharing regions");
for (int i = 0; i < selectControlList.Count; i++)
{
for (int j = i + 1; j < selectControlList.Count; j++)
{
((Individual)controlIndividualList[selectControlList[i]]).PairwiseComparison(wholePairwiseIBDRegionList, (Individual)controlIndividualList[selectControlList[j]], (Block[])newBlockDictionary.blockList.ToArray(typeof(Block)), newMapData, newCommands.cut, windowStart, windowEnd);
}
Console.SetCursorPosition(16, Console.CursorTop);
Console.Write("{0} / {1}\tTotal regions: {2}", i + 1, selectControlList.Count, wholePairwiseIBDRegionList.Count);
}
Console.WriteLine("\t\tFinished.");
MyIBDComparer newComparer = new MyIBDComparer();
wholePairwiseIBDRegionList.Sort(newComparer);
GroupShareFinder newIBDList = new GroupShareFinder(wholePairwiseIBDRegionList);
Console.WriteLine("\t\tSrart searching for group sharing regions: ");
newIBDList.findGroupIBD(controlIndividualList, newBlockDictionary, controlLinkageData, newResultList, resultList, windowStart, windowEnd);
finalResultList.AddNewControlList(newResultList, caseData.individual.Length, 0.2);
}
}
Console.WriteLine("Finished permutation in controls");
finalResultList.CalculateControlResultParameters();
Console.WriteLine("Finished puermutation result calculation");
caseData.SetIndividualList(caseIndividualList);
caseData = null;
GC.Collect();
Console.WriteLine("Haplotyping for all case samples...");
for (int indIndex = 0; indIndex < caseIndividualList.Count; indIndex++)
{
((Individual)(caseIndividualList[indIndex])).SetIndividualID(indIndex);
}
ind = 0;
foreach (Individual newIndividual in caseIndividualList) //haplotyping for each individual.
{
newIndividual.Haplotyping(newBlockDictionary, newMapData, controlLinkageData);
ind++;
Console.SetCursorPosition(8, Console.CursorTop);
Console.Write("{0} / {1}", ind, caseIndividualList.Count);
}
Console.Write("\t\tFinished.\n");
for (int n = 0; n < 1; n++) //case evaluation
{
Console.Write("\tTotally {0} blocks will be analyzed.\n", newBlockDictionary.blockList.Count);
List <GroupShare> resultList = new List <GroupShare>(); //unfinished result from last window
for (int windowStart = 0; windowStart <= newBlockDictionary.blockList.Count - 1; windowStart += 30000)
{
List <GroupShare> newResultList = new List <GroupShare>();
int windowEnd = Math.Min(windowStart + 30000, newBlockDictionary.blockList.Count - 1);
Console.WriteLine("\tAnalyzing block {0} to {1}", windowStart, windowEnd - 1);
ArrayList wholePairwiseIBDRegionList = new ArrayList();
Console.WriteLine("\t\tSearching for pairwise sharing regions");
for (int i = 0; i < caseIndividualList.Count; i++)
{
for (int j = i + 1; j < caseIndividualList.Count; j++)
{
((Individual)caseIndividualList[i]).PairwiseComparison(wholePairwiseIBDRegionList, (Individual)caseIndividualList[j], (Block[])newBlockDictionary.blockList.ToArray(typeof(Block)), newMapData, newCommands.cut, windowStart, windowEnd);
}
Console.SetCursorPosition(16, Console.CursorTop);
Console.Write("{0} / {1}\tTotal regions: {2}", i + 1, caseIndividualList.Count, wholePairwiseIBDRegionList.Count);
}
Console.WriteLine("\n\t\tFinished searching pairwise sharing regions");
MyIBDComparer newComparer = new MyIBDComparer();
wholePairwiseIBDRegionList.Sort(newComparer);
GroupShareFinder newIBDList = new GroupShareFinder(wholePairwiseIBDRegionList);
Console.WriteLine("\t\tSrart searching for group sharing regions:");
newIBDList.findGroupIBD(caseIndividualList, newBlockDictionary, controlLinkageData, newResultList, resultList, windowStart, windowEnd);
finalResultList.calculateAllPvalue(newResultList, caseIndividualList.Count, 0.2, newCommands);
finalResultList.Combine(newResultList);
finalResultList.ClearReplication();
}
}
finalResultList.PrintResult(newBlockDictionary, caseIndividualList.Count, 0.2, newCommands);
}
public void Evalation(GeneticDistance newGeneticDistance, MapData newMapData, BlockDictionary newBlockDictionary, Commands newCommands)
{
ResultList finalResultList = new ResultList();
finalResultList.SetpTable();
CaseControlEvaluation(newGeneticDistance, newMapData, newBlockDictionary, newCommands, finalResultList);
}
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--;
}
}
}
