public bool Add(CalledAllele nextVariant, string issueLogPath)
{
UpdateBuffer(nextVariant);
//Check the buffer, and see if we passed an amplicon edge in our window.
//If we did, then we are interested in this window. In particular, at the variant in the middle of it.
if (DidWeDetectAnEdge(_testIndex, _trailingAlleleBuffer))
{
var AlleleOfInterest = _trailingAlleleBuffer[_testIndex]; //we keep this as a class, to do the math on
var category = MutationCategoryUtil.GetMutationCategory(AlleleOfInterest.ReferenceAllele, AlleleOfInterest.AlternateAllele);
NumPossibleVariants++;
if (category != MutationCategory.Reference)
{
CountsByCategory[category]++;
File.AppendAllText(issueLogPath, AlleleOfInterest + Environment.NewLine);
return(true);
}
}
return(false);
}
public CountData()
{
var categories = MutationCategoryUtil.GetAllMutationCategories();
foreach (var nucleotideTransitionCategory in categories)
{
CountsByCategory.Add(nucleotideTransitionCategory, 0);
}
}
public bool Add(CalledAllele variant)
{
if (variant == null)
{
return(false);
}
var category = MutationCategoryUtil.GetMutationCategory(variant);
NumPossibleVariants++;
if (category != MutationCategory.Reference)
{
CountsByCategory[category]++;
return(true);
}
return(false);
}
/// <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);
}
