private static MutationCategory LoadCategoryNode(XmlTextReader stream)
{
MutationCategory mutationCategory = new MutationCategory
{
Name = stream.GetAttribute("Name"),
DisplayName = stream.GetAttribute("DisplayName"),
Help = stream.GetAttribute("Help"),
Stat = stream.GetAttribute("Stat"),
Property = stream.GetAttribute("Property"),
ForceProperty = stream.GetAttribute("ForceProperty")
};
while (stream.Read())
{
if (stream.Name == "mutation")
{
MutationEntry mutationEntry = Egcb_MutableMutations.LoadMutationNode(stream);
mutationEntry.Category = mutationCategory;
if (!mutationEntry.Prerelease || Options.GetOption("OptionEnablePrereleaseContent", string.Empty) == "Yes")
{
mutationCategory.Entries.Add(mutationEntry);
}
}
if (stream.NodeType == XmlNodeType.EndElement && (stream.Name == string.Empty || stream.Name == "category"))
{
return(mutationCategory);
}
}
return(mutationCategory);
}
public double MutationRateForCategory(MutationCategory cat)
{
if (CountsByCategory.ContainsKey(cat))
{
return(((double)CountsByCategory[cat]) / NumPossibleVariants);
}
else
{
return(0);
}
}
//Most of LoadVanillaMutations, LoadCategoryNode, and LoadMutationNode were adapted directly from the game's MutationFactory code
private static void LoadVanillaMutations()
{
Egcb_MutableMutations.MutationData.Clear();
Egcb_MutableMutations.MutationCategoryDict.Clear();
using (XmlTextReader stream = DataManager.GetStreamingAssetsXMLStream("Mutations.xml"))
{
stream.WhitespaceHandling = WhitespaceHandling.None;
while (stream.Read())
{
if (stream.Name == "mutations")
{
while (stream.Read())
{
if (stream.Name == "category")
{
MutationCategory mutationCategory = Egcb_MutableMutations.LoadCategoryNode(stream);
if (mutationCategory.Name[0] == '-')
{
if (Egcb_MutableMutations.MutationCategoryDict.ContainsKey(mutationCategory.Name.Substring(1)))
{
MutationCategory cat = MutationFactory.CategoriesByName[mutationCategory.Name.Substring(1)];
Egcb_MutableMutations.MutationCategoryDict.Remove(mutationCategory.Name.Substring(1));
Egcb_MutableMutations.MutationData.Remove(cat);
}
}
else if (Egcb_MutableMutations.MutationCategoryDict.ContainsKey(mutationCategory.Name))
{
Egcb_MutableMutations.MutationCategoryDict[mutationCategory.Name].MergeWith(mutationCategory);
}
else
{
Egcb_MutableMutations.MutationCategoryDict.Add(mutationCategory.Name, mutationCategory);
Egcb_MutableMutations.MutationData.Add(mutationCategory);
}
}
if (stream.NodeType == XmlNodeType.EndElement && (stream.Name == string.Empty || stream.Name == "mutations"))
{
break;
}
}
}
if (stream.NodeType == XmlNodeType.EndElement && (stream.Name == string.Empty || stream.Name == "mutations"))
{
break;
}
}
stream.Close();
}
}
private Species GenerateInitialSpecies(EaterType eaterType, float calorieLimit)
{
List <Mutation> heads = AllMutations.Where(mutation => {
HeadMutation head = mutation as HeadMutation;
return(head != null && head.Type == eaterType);
}).ToList();
List <Mutation> remainingMutations = AllMutations.Where(mutation => {
return(!(mutation is HeadMutation) && !(mutation is TorsoMutation));
}).ToList();
Species newSpecies = new Species("Species");
newSpecies.AddMutation(_torsos[Random.Range(0, _torsos.Count)]);
newSpecies.AddMutation(heads[Random.Range(0, heads.Count)]);
while (remainingMutations.Count > 0 && newSpecies.CalorieConsumption < calorieLimit)
{
Mutation newMutation = remainingMutations[Random.Range(0, remainingMutations.Count)];
newSpecies.AddMutation(newMutation);
for (int i = remainingMutations.Count - 1; i >= 0; i--)
{
MutationCategory category = remainingMutations[i].Category;
if (category != null && category == newMutation.Category)
{
remainingMutations.RemoveAt(i);
}
}
}
newSpecies.OnResearchComplete += OnResearchComplete;
Species.Add(newSpecies);
BeginRandomResearch(newSpecies);
return(newSpecies);
}
/// <summary>
/// This is a pretty naive reader. The mutation categories must be listed first, and the rates must be listed last, or the parsing fails.
/// There are some hard coded strings. Yes, maybe it should be in json.
/// </summary>
/// <param name="file"></param>
/// <returns></returns>
public static CountData ReadCountsFile(string file)
{
CountData variantCounts = new CountData();
bool inRateSection = false;
using (StreamReader sr = new StreamReader(new FileStream(file, FileMode.Open)))
{
string line;
while (true)
{
line = sr.ReadLine();
if (line == "")
{
continue;
}
if (line == null)
{
break;
}
if (inRateSection)
{
string[] splat = line.Split();
if (splat.Length < 2)
{
continue;
}
double result = -1;
if (!(double.TryParse(splat[1], out result)))
{
throw new IOException("Unable to parse counts from noise file " + file);
}
string firstWord = splat[0];
switch (firstWord)
{
case "AllPossibleVariants":
variantCounts.NumPossibleVariants += result;
break;
case "FalsePosVariantsFound":
case "ErrorRate(%)":
case "VariantsCountedTowardEstimate":
case "ErrorRateEstimate(%)":
case "MismatchEstimate(%)":
continue;
default:
//if its a mutation category - do something. Else do nothing
if (MutationCategoryUtil.IsValidCategory(firstWord))
{
MutationCategory category = MutationCategoryUtil.GetMutationCategory(firstWord);
//this category should always exist. this is just defensive
if (!variantCounts.CountsByCategory.ContainsKey(category))
{
variantCounts.CountsByCategory.Add(category, 0);
Logger.WriteWarningToLog("This counts file found a mutation category listed that this version of VQR is not aware of, and cannot process. Please check " + firstWord);
}
variantCounts.CountsByCategory[category] += result;
}
break;
}
}
if (line.Contains("CountsByCategory"))
{
inRateSection = true;
}
}
}
return(variantCounts);
}
public static void InsertNewQ(Dictionary <MutationCategory, int> qCalibratedRates, CalledAllele originalVar, MutationCategory cat, int newQ, bool isSomatic)
{
originalVar.VariantQscore = newQ;
originalVar.NoiseLevelApplied = qCalibratedRates[cat];
if (isSomatic)
{
originalVar.GenotypeQscore = newQ;
}
}
public static void UpdateVariantQScoreAndRefilter(int maxQscore, int filterQScore, Dictionary <MutationCategory, int> qCalibratedRates, CalledAllele originalVar, MutationCategory cat,
bool subsample)
{
double depth;
double callCount;
//tjd+
// We can revisit this math at a later date. Exactly how we lower the Qscores
// or filter the suspect calls is TBD. We should work with this new algorithm
// on a larger collection of datasets representing various alignment issues,
// and modify the code/parameters as needed.
// A few thoughts: Amplicon edge issues don't get better the deeper you sequence.
// We need to scale out depth from the Q score calculation (since the original Q score is a fxn of depth/freq).
// One option is to Cap at ~100 DP (TODO, this should be a parameter, a fxn of your bascallquality).
// double subSampleToThis = 100;
// tjd-
double denominator = MathOperations.QtoP(qCalibratedRates[cat]);
double subSampleToThis = 1.0 / denominator;
if ((qCalibratedRates[cat] == 0) || (denominator == 0))
{
subsample = false;
}
bool canUpdateQ = HaveInfoToUpdateQ(originalVar, out depth, out callCount);
if (subsample && (depth > subSampleToThis))
{
callCount = callCount * subSampleToThis / depth;
depth = subSampleToThis;
}
if (canUpdateQ)
{
int newQ = VariantQualityCalculator.AssignPoissonQScore(
(int)callCount, (int)depth, qCalibratedRates[cat], Math.Min(originalVar.VariantQscore, maxQscore)); //note, using "originalVar.VariantQscore" and the maxQ stops us from ever RAISING the q score over these values.
InsertNewQ(qCalibratedRates, originalVar, cat, newQ, true);
//update filters if needed
if (newQ < filterQScore)
{
if (originalVar.Filters.Contains(FilterType.LowVariantQscore))
{
return;
}
originalVar.Filters.Add(FilterType.LowVariantQscore);
}
}
}
public static void InsertNewQ(Dictionary <MutationCategory, int> qCalibratedRates, VcfVariant originalVar, MutationCategory cat, int newQ)
{
originalVar.Quality = newQ;
if (originalVar.Genotypes[0].ContainsKey("GQ"))
{
originalVar.Genotypes[0]["GQ"] = newQ.ToString();
}
if (originalVar.Genotypes[0].ContainsKey("GQX"))
{
originalVar.Genotypes[0]["GQX"] = newQ.ToString();
}
if (originalVar.Genotypes[0].ContainsKey("NL"))
{
originalVar.Genotypes[0]["NL"] = qCalibratedRates[cat].ToString();
}
}
public static void UpdateVariant(int maxQscore, int filterQScore, Dictionary <MutationCategory, int> qCalibratedRates, VcfVariant originalVar, MutationCategory cat)
{
int depth;
int callCount;
bool canUpdateQ = HaveInfoToUpdateQ(originalVar, out depth, out callCount);
if (canUpdateQ)
{
int newQ = VariantQualityCalculator.AssignPoissonQScore(
callCount, depth, qCalibratedRates[cat], maxQscore);
InsertNewQ(qCalibratedRates, originalVar, cat, newQ);
//update filters if needed
if (newQ < filterQScore)
{
var vcfConfig = new VcfWriterConfig();
vcfConfig.VariantQualityFilterThreshold = filterQScore;
var formatter = new VcfFormatter(vcfConfig);
string lowQString = formatter.MapFilter(FilterType.LowVariantQscore);
string passString = VcfFormatter.PassFilter;
if (originalVar.Filters.Contains(lowQString))
{
return;
}
if (originalVar.Filters == passString)
{
originalVar.Filters = lowQString;
}
else
{
originalVar.Filters += VcfFormatter.FilterSeparator + lowQString;
}
}
}
}
public void LoadCountsFile(string file)
{
bool inRateSection = false;
using (StreamReader sr = new StreamReader(file))
{
string line;
while (true)
{
line = sr.ReadLine();
if (line == "")
{
continue;
}
if (line == null)
{
break;
}
if (inRateSection)
{
string[] Splat = line.Split();
if (Splat.Length < 2)
{
continue;
}
double result = -1;
if (!(double.TryParse(Splat[1], out result)))
{
throw new ApplicationException("Unable to parse counts from noise file " + file);
}
switch (Splat[0])
{
case "AllPossibleVariants":
NumPossibleVariants += result;
break;
case "FalsePosVariantsFound":
case "ErrorRate(%)":
case "VariantsCountedTowardEstimate":
case "ErrorRateEstimate(%)":
case "MismatchEstimate(%)":
continue;
default:
MutationCategory category = MutationCounter.GetMutationCategory(Splat[0]);
CountsByCategory[category] += result;
break;
}
}
if (line.Contains("CountsByCategory"))
{
inRateSection = true;
}
}
}
}