Пример #1
0
        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));
        }
Пример #2
0
 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));
 }
Пример #3
0
 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));
 }
Пример #4
0
 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));
 }
Пример #5
0
        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));
        }
Пример #6
0
        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));
        }