public FKPM(double fkpm, double hi, double lo, BioSample samp) { Sample = samp; FKPMCount = fkpm; HI = hi; LO = lo; }
protected static void SendToStaticFKPM(PreSampleDefinition p, BioSample bios) { bios.HasExprs = true; if (LatestFKPMColIndexed == null) { LatestFKPMColIndexed = new Dictionary <string, BioSample[]> (); } foreach (string st in p.FileNames) { if (!LatestFKPMColIndexed.ContainsKey(st)) { LatestFKPMColIndexed.Add(st, new BioSample[p.TotalColumns]); } foreach (int ii in p.ColIDs) { int index = ii - 9; if (index != 0) { index /= 4; } LatestFKPMColIndexed [st] [index] = bios; } } hasFKPMSomethingToLoad = true; }
public static void Assemble() { Genome = new Genome(); ProgramState.Init(); AppSettings.Assemble(); RankSplit.Assemble(); FPKMFileNames = new List <string> (); BAMFileNames = new List <string> (); VariantFileNames = new List <string> (); TypeDict = new ElementTypeDictionary(); Samples = new Dictionary <string, BioSample> (); BioSample.ResetStaticLoader(); GeneToScaffDict = new Dictionary <string, string> (); RegionToScaffDict = new Dictionary <string, string> (); RSPToMergeSeries = new List <Series> (); StatsTester.Assemble(); }
private static void RunSampleAllocationLoading(object ob) { try { BioSample.ResetStaticLoader(); List <PreSampleDefinition> prel = (List <PreSampleDefinition>)ob; foreach (PreSampleDefinition pre in prel) { if (!Samples.ContainsKey(pre.ID)) { Samples.Add(pre.ID, new BioSample(pre.ID)); } Samples [pre.ID].RecieveDefinition(pre); } BioSample.LoadAllStatic(); } catch (Exception e) { ShowMessageWindow(e.Message, true); } }
protected static void SendToStatic(PreSampleDefinition p, BioSample bios) { bios.HasVars = true; if (LatestVarColIndexed == null) { LatestVarColIndexed = new Dictionary <string, BioSample[]> (); } if (IsGenotypedNames == null) { IsGenotypedNames = new Dictionary <string, bool> (); } if (p.IsGenotyped) { if (!LatestVarColIndexed.ContainsKey(p.FileNames [0])) { LatestVarColIndexed.Add(p.FileNames [0], new BioSample[p.TotalColumns]); } foreach (int ii in p.ColIDs) { LatestVarColIndexed [p.FileNames [0]] [ii - 9] = bios; } if (!IsGenotypedNames.ContainsKey(p.FileNames [0])) { IsGenotypedNames.Add(p.FileNames [0], p.IsGenotyped); } } else { foreach (string s in p.FileNames) { if (!IsGenotypedNames.ContainsKey(s)) { IsGenotypedNames.Add(s, p.IsGenotyped); } } } hasVarSomethingToLoad = true; }
public NameRead(BioSample samp, int _start, int _end, string name) : base(samp, _start, _end) { Name = name; }
public NameRead(BioSample samp, string name) : base(samp) { Name = name; }
public SeqRead(BioSample samp, int _start, int _end) { Sample = samp; Start = _start; End = _end; }
public SeqRead(BioSample samp) { Sample = samp; }
public SampleVariant(int ma, int alt, BioSample bio) { MajorInd = ma; AltInd = alt; BioS = bio; }