private Action <JsonObject, List <string[]> > GetJsonStringGenerationAction()
{
var actions = new List <Action <JsonObject, string[]> >();
foreach (string key in Keys)
{
if (NonSaKeys.Contains(key))
{
continue;
}
var intendedType = GetJsonType(key);
if (intendedType.Equals(SaJsonValueType.String))
{
actions.Add((jsonObject, value) => CountKeyIfAdded(jsonObject.AddStringValue(key, value[0]), key));
}
else if (intendedType.Equals(SaJsonValueType.Bool))
{
actions.Add((jsonObject, value) => CountKeyIfAdded(jsonObject.AddBoolValue(key, CheckAndGetBoolFromString(value[0])), key));
}
else if (intendedType.Equals(SaJsonValueType.Number))
{
actions.Add((jsonObject, value) =>
{
if (value[0] == null)
{
return;
}
var doubleValue = CheckAndGetNullableDoubleFromString(value[0]);
CustomAnnotationCategories keyCategory = GetCategory(key);
CountKeyIfAdded(keyCategory == CustomAnnotationCategories.AlleleFrequency
? jsonObject.AddDoubleValue(key, doubleValue, "0.######")
: jsonObject.AddStringValue(key, value[0], false), key);
});
}
else if (intendedType.Equals(SaJsonValueType.StringArray))
{
actions.Add((jsonObject, value) => CountKeyIfAdded(jsonObject.AddStringValues(key, value), key));
}
else
{
throw new Exception($"Unknown data type {intendedType}");
}
}
return((jsonObject, strings) =>
{
foreach (var(action, str) in actions.Zip(strings, (a, b) => (a, b)))
{
action(jsonObject, str);
}
TotalItems++;
});
}
public SaJsonKeyProperties(SaJsonValueType valueType, CustomAnnotationCategories category, string description)
{
ValueType = valueType;
Category = category;
Description = description;
}
public static SaJsonKeyAnnotation CreateFromProperties(SaJsonValueType valueType, CustomAnnotationCategories category, string description)
{
return(new SaJsonKeyAnnotation {
Properties = new SaJsonKeyProperties(valueType, category, description)
});
}
public static CustomAnnotationCategories[] ParseCategories(string line, int numRequiredColumns, int numAnnotationColumns, Action <string, string>[] annotationValidators, string rowNumber)
{
CheckPrefix(line, "#categories", rowNumber);
var splits = line.OptimizedSplit('\t');
if (splits.Length != numRequiredColumns + numAnnotationColumns)
{
throw new UserErrorException("#categories row must have the same number of columns as the header row with column names.");
}
var categories = new CustomAnnotationCategories[numAnnotationColumns];
for (var i = 0; i < numAnnotationColumns; i++)
{
switch (splits[i + numRequiredColumns].ToLower())
{
case "allelecount":
categories[i] = CustomAnnotationCategories.AlleleCount;
break;
case "allelenumber":
categories[i] = CustomAnnotationCategories.AlleleNumber;
break;
case "allelefrequency":
categories[i] = CustomAnnotationCategories.AlleleFrequency;
break;
case "homozygouscount":
categories[i] = CustomAnnotationCategories.HomozygousCount;
break;
case "prediction":
categories[i] = CustomAnnotationCategories.Prediction;
annotationValidators[i] = AllowedValues.ValidatePredictionValue;
break;
case "filter":
categories[i] = CustomAnnotationCategories.Filter;
annotationValidators[i] = AllowedValues.ValidateFilterValue;
break;
case "identifier":
categories[i] = CustomAnnotationCategories.Identifier;
annotationValidators[i] = AllowedValues.ValidateIdentifierValue;
break;
case "description":
categories[i] = CustomAnnotationCategories.Description;
annotationValidators[i] = AllowedValues.ValidateDescriptionValue;
break;
case ".":
case "":
categories[i] = CustomAnnotationCategories.Unknown;
break;
default:
throw new UserErrorException($"Invalid category value: {splits[i + numRequiredColumns]}");
}
}
return(categories);
}
