internal ExecutionReport Cover(
CoverVariation coverVariation,
char strand, int minAcc, int maxAcc, Aggregate aggregate,
out FunctionOutput <Output <C, I, M> > result,
MaxDegreeOfParallelism maxDegreeOfParallelism)
{
int totalBookmarks = 0;
var tmpResult = new FunctionOutput <Output <C, I, M> >();
foreach (var chr in chrs)
{
foreach (var sDi4 in chr.Value)
{
if (!tmpResult.Chrs.ContainsKey(chr.Key))
{
tmpResult.Chrs.TryAdd(chr.Key, new ConcurrentDictionary <char, List <Output <C, I, M> > >());
}
if (!tmpResult.Chrs[chr.Key].ContainsKey(sDi4.Key))
{
tmpResult.Chrs[chr.Key].TryAdd(sDi4.Key, new List <Output <C, I, M> >());
}
}
}
_stpWtch.Restart();
Parallel.ForEach(chrs,
new ParallelOptions {
MaxDegreeOfParallelism = maxDegreeOfParallelism.chrDegree
},
chr =>
{
IOutput <C, I, M, Output <C, I, M> > outputStrategy = new AggregateFactory <C, I, M>().GetAggregateFunction(aggregate);
foreach (var sDi4 in chr.Value)
{
totalBookmarks += sDi4.Value.bookmarkCount;
switch (coverVariation)
{
case CoverVariation.Cover:
sDi4.Value.Cover <Output <C, I, M> >(outputStrategy, minAcc, maxAcc, maxDegreeOfParallelism.di4Degree);
break;
case CoverVariation.Summit:
sDi4.Value.Summit <Output <C, I, M> >(outputStrategy, minAcc, maxAcc, maxDegreeOfParallelism.di4Degree);
break;
}
tmpResult.Chrs[chr.Key][sDi4.Key] = outputStrategy.output;
}
});
_stpWtch.Stop();
result = tmpResult;
return(new ExecutionReport(totalBookmarks, _stpWtch.Elapsed));
}
public ExecutionReport VariantAnalysis(char strand, Dictionary <string, Dictionary <char, List <I> > > references, Aggregate aggregate, out FunctionOutput <Output <C, I, M> > result, MaxDegreeOfParallelism maxDegreeOfParallelism, out Dictionary <uint, int> newRes)
{
return(genome.VariantAnalysis(references, strand, aggregate, out result, out newRes, maxDegreeOfParallelism));
}
public ExecutionReport Map(char strand, Dictionary <string, Dictionary <char, List <I> > > references, Aggregate aggregate, out FunctionOutput <Output <C, I, M> > result, MaxDegreeOfParallelism maxDegreeOfParallelism)
{
return(genome.Map(references, strand, aggregate, out result, maxDegreeOfParallelism));
}
public ExecutionReport Cover(CoverVariation coverVariation, char strand, int minAcc, int maxAcc, Aggregate aggregate, out FunctionOutput <Output <C, I, M> > result, MaxDegreeOfParallelism maxDegreeOfParallelism)
{
return(genome.Cover(coverVariation, strand, minAcc, maxAcc, aggregate, out result, maxDegreeOfParallelism));
}
internal ExecutionReport VariantAnalysis(
Dictionary <string, Dictionary <char, List <I> > > references,
char strand, Aggregate aggregate,
out FunctionOutput <Output <C, I, M> > result,
out Dictionary <uint, int> newRes,
MaxDegreeOfParallelism maxDegreeOfParallelism)
{
int totalIntervals = 0;
var tmpResults = new FunctionOutput <Output <C, I, M> >();
foreach (var refChr in references)
{
if (!chrs.ContainsKey(refChr.Key))
{
continue;
}
foreach (var refStrand in refChr.Value)
{
if (!chrs[refChr.Key].ContainsKey(refStrand.Key))
{
continue;
}
if (!tmpResults.Chrs.ContainsKey(refChr.Key))
{
tmpResults.Chrs.TryAdd(refChr.Key, new ConcurrentDictionary <char, List <Output <C, I, M> > >());
}
if (!tmpResults.Chrs[refChr.Key].ContainsKey(refStrand.Key))
{
tmpResults.Chrs[refChr.Key].TryAdd(refStrand.Key, new List <Output <C, I, M> >());
}
}
}
string lockOnMe = "Vahid";
Dictionary <uint, int> tmpRes = new Dictionary <uint, int>();
_stpWtch.Restart();
Parallel.ForEach(references,
new ParallelOptions {
MaxDegreeOfParallelism = maxDegreeOfParallelism.chrDegree
},
refChr =>
{
IOutput <C, I, M, Output <C, I, M> > outputStrategy = new VariantAnalysisOutputStrategy <C, I, M>();
if (chrs.ContainsKey(refChr.Key))
{
foreach (var refStrand in refChr.Value)
{
if (!chrs[refChr.Key].ContainsKey(refStrand.Key))
{
continue;
}
chrs[refChr.Key][refStrand.Key].VariantAnalysis <Output <C, I, M> >(ref outputStrategy, refStrand.Value, maxDegreeOfParallelism.di4Degree);
tmpResults.Chrs[refChr.Key][refStrand.Key] = outputStrategy.output;
totalIntervals += refStrand.Value.Count;
lock (lockOnMe)
{
foreach (var item in ((VariantAnalysisOutputStrategy <C, I, M>)outputStrategy).samplesCV)
{
if (tmpRes.ContainsKey(item.Key))
{
tmpRes[item.Key] += item.Value;
}
else
{
tmpRes.Add(item.Key, item.Value);
}
}
}
}
}
});
_stpWtch.Stop();
result = tmpResults;
newRes = tmpRes;
return(new ExecutionReport(totalIntervals, _stpWtch.Elapsed));
}
internal ExecutionReport Map(
Dictionary <string, Dictionary <char, List <I> > > references,
char strand, Aggregate aggregate,
out FunctionOutput <Output <C, I, M> > result,
MaxDegreeOfParallelism maxDegreeOfParallelism)
{
int totalIntervals = 0;
var tmpResults = new FunctionOutput <Output <C, I, M> >();
foreach (var refChr in references)
{
if (!chrs.ContainsKey(refChr.Key))
{
continue;
}
foreach (var refStrand in refChr.Value)
{
if (!chrs[refChr.Key].ContainsKey(refStrand.Key))
{
continue;
}
if (!tmpResults.Chrs.ContainsKey(refChr.Key))
{
tmpResults.Chrs.TryAdd(refChr.Key, new ConcurrentDictionary <char, List <Output <C, I, M> > >());
}
if (!tmpResults.Chrs[refChr.Key].ContainsKey(refStrand.Key))
{
tmpResults.Chrs[refChr.Key].TryAdd(refStrand.Key, new List <Output <C, I, M> >());
}
}
}
_stpWtch.Restart();
Parallel.ForEach(references,
new ParallelOptions {
MaxDegreeOfParallelism = maxDegreeOfParallelism.chrDegree
},
refChr =>
{
IOutput <C, I, M, Output <C, I, M> > outputStrategy = new AggregateFactory <C, I, M>().GetAggregateFunction(aggregate);
if (chrs.ContainsKey(refChr.Key))
{
foreach (var refStrand in refChr.Value)
{
if (!chrs[refChr.Key].ContainsKey(refStrand.Key))
{
continue;
}
chrs[refChr.Key][refStrand.Key].Map <Output <C, I, M> >(ref outputStrategy, refStrand.Value, maxDegreeOfParallelism.di4Degree);
tmpResults.Chrs[refChr.Key][refStrand.Key] = outputStrategy.output;
totalIntervals += refStrand.Value.Count;
}
}
});
_stpWtch.Stop();
result = tmpResults;
return(new ExecutionReport(totalIntervals, _stpWtch.Elapsed));
}
