public void Coverage(ArrayList rareBlockList, SnpDataSet dataSet)
{
int[] coverage = new int[dataSet.GetSnpCount()];
int total = 0;
foreach (RareBlock rareBlock in rareBlockList)
{
for (int i = rareBlock.start; i <= rareBlock.end; i++)
{
coverage[i] = 1;
}
}
foreach (int i in coverage)
{
if (i == 1)
{
total++;
}
}
Console.WriteLine(total);
}
public void Extend(SnpDataSet dataSet)
{
int newStart = this.GetStart();
int newEnd = this.GetEnd();
ArrayList newEndingSequence = new ArrayList();
while (newEnd < dataSet.GetSnpCount() - 1)
{
int data = -1;
bool flag = false;
for (int i = 1; i < this.group.Length; i++)
{
if (data == -1)
{
if (dataSet.GetSnp(this.group[i], newEnd + 1) != 1)
{
data = dataSet.GetSnp(this.group[i], newEnd + 1);
}
}
else if (Math.Abs(dataSet.GetSnp(this.group[i], newEnd + 1) - data) == 2)
{
flag = true;
break;
}
}
if (flag)
{
break;
}
if (data == -1)
{
newEndingSequence.Add(1);
}
else if (data == 0)
{
newEndingSequence.Add(0);
}
else
{
newEndingSequence.Add(2);
}
newEnd++;
}
ArrayList newStartingSequence = new ArrayList();
while (newStart > 0)
{
int data = -1;
bool flag = false;
for (int i = 1; i < this.GetGroup().Length; i++)
{
if (data == -1)
{
if (dataSet.GetSnp(this.group[i], newStart - 1) != 1)
{
data = dataSet.GetSnp(this.group[i], newStart - 1);
}
}
else if (Math.Abs(dataSet.GetSnp(this.group[i], newStart - 1) - data) == 2)
{
flag = true;
break;
}
}
if (flag)
{
break;
}
if (data == -1)
{
newStartingSequence.Add(1);
}
else if (data == 0)
{
newStartingSequence.Add(0);
}
else
{
newStartingSequence.Add(2);
}
newStart--;
}
newStartingSequence.Reverse();
int[] newWholeSequence = new int[this.sequence.Length + newStartingSequence.Count + newEndingSequence.Count];
newStartingSequence.CopyTo(newWholeSequence);
this.GetSequence().CopyTo(newWholeSequence, newStartingSequence.Count);
newEndingSequence.CopyTo(newWholeSequence, newStartingSequence.Count + this.sequence.Length);
this.SetSequence(newWholeSequence);
this.SetStart(newStart);
this.SetEnd(newEnd);
if (this.GetEnd() - this.GetEnd() > 170)
{
;
}
while (newEnd < dataSet.GetSnpCount())
{
ArrayList group0 = new ArrayList();
ArrayList group1 = new ArrayList();
ArrayList group2 = new ArrayList();
for (int i = 0; i < this.GetGroup().Length; i++)
{
if (this.GetGroup(i) == 0)
{
group0.Add(this.GetGroup(i));
}
else if (this.GetGroup(i) == 2)
{
group2.Add(this.GetGroup(i));
}
else
{
group1.Add(this.GetGroup(i));
}
}
}
}
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);
}
