public ClinGenItem(string id, IChromosome chromosome, int start, int end, VariantType variantType, int observedGains, int observedLosses,
ClinicalInterpretation clinicalInterpretation, bool validated, HashSet <string> phenotypes = null, HashSet <string> phenotypeIds = null)
{
Id = id;
Chromosome = chromosome;
Start = start;
End = end;
VariantType = variantType;
ClinicalInterpretation = clinicalInterpretation;
_phenotypes = phenotypes ?? new HashSet <string>();
_phenotypeIds = phenotypeIds ?? new HashSet <string>();
ObservedGains = observedGains;
ObservedLosses = observedLosses;
Validated = validated;
}
public override int GetHashCode()
{
unchecked
{
var hashCode = Id?.GetHashCode() ?? 0;
hashCode = (hashCode * 397) ^ (Chromosome?.GetHashCode() ?? 0);
hashCode = (hashCode * 397) ^ Start.GetHashCode();
hashCode = (hashCode * 397) ^ End.GetHashCode();
hashCode = (hashCode * 397) ^ VariantType.GetHashCode();
hashCode = (hashCode * 397) ^ Validated.GetHashCode();
hashCode = (hashCode * 397) ^ ObservedGains.GetHashCode();
hashCode = (hashCode * 397) ^ ClinicalInterpretation.GetHashCode();
hashCode = (hashCode * 397) ^ ObservedLosses.GetHashCode();
return(hashCode);
}
}
private static string GetClinicalDescription(ClinicalInterpretation clinicalInterpretation)
{
switch (clinicalInterpretation)
{
case ClinicalInterpretation.uncertain_significance:
return("uncertain significance");
case ClinicalInterpretation.likely_benign:
return("likely benign");
case ClinicalInterpretation.likely_pathogenic:
return("likely pathogenic");
default:
return(clinicalInterpretation.ToString());
}
}
private static string GetClinicalDescription(ClinicalInterpretation clinicalInterpretation)
{
// ReSharper disable once SwitchStatementMissingSomeCases
switch (clinicalInterpretation)
{
case ClinicalInterpretation.uncertain_significance:
return("uncertain significance");
case ClinicalInterpretation.likely_benign:
return("likely benign");
case ClinicalInterpretation.likely_pathogenic:
return("likely pathogenic");
case ClinicalInterpretation.unknown:
return(null);
default:
return(clinicalInterpretation.ToString());
}
}
public void MergeItem(ClinGenItem other)
{
//sanity check
if (!Id.Equals(other.Id) || !Chromosome.Equals(other.Chromosome) || Start != other.Start || End != other.End)
{
throw new Exception($"different region with same parent ID {Id}\n");
}
//check if the validate status and clinical interpretation are consistent
if (Validated || other.Validated)
{
Validated = true;
}
if (!ClinicalInterpretation.Equals(other.ClinicalInterpretation))
{
if (ClinicalInterpretation < other.ClinicalInterpretation)
{
ClinicalInterpretation = other.ClinicalInterpretation;
}
}
if (other.VariantType == VariantType.copy_number_gain)
{
ObservedGains++;
}
else if (other.VariantType == VariantType.copy_number_loss)
{
ObservedLosses++;
}
foreach (var phenotype in other.Phenotypes)
{
_phenotypes.Add(phenotype);
}
foreach (var phenotypeId in other.PhenotypeIds)
{
_phenotypeIds.Add(phenotypeId);
}
}
private static void ParseInfor(string tagFiled, string infoField, out string id, out VariantType variantType,
out int observedGains, out int observedLosses, out ClinicalInterpretation clinicalInterpretation, out bool validated,
out HashSet <string> phenotypes, out HashSet <string> phenotypeIds)
{
id = null;
variantType = VariantType.unknown;
observedGains = 0;
observedLosses = 0;
clinicalInterpretation = ClinicalInterpretation.unknown;
validated = false;
phenotypes = new HashSet <string>();
phenotypeIds = new HashSet <string>();
var tags = tagFiled.Split(',');
var info = infoField.Split(',');
if (tags.Length != info.Length)
{
throw new Exception("Unequal length of attrTags and attrVals\n");
}
var len = tags.Length;
for (var i = 0; i < len; i++)
{
switch (tags[i])
{
case IdTag:
id = info[i];
break;
case ClinicalInterpretationTag:
clinicalInterpretation = ParseClinicalInterpretation(info[i]);
break;
case ValidatedTag:
validated = info[i].Equals("Pass");
break;
case VariantTypeTag:
variantType = GetVariantType(info[i]);
break;
case PhenotypeTag:
phenotypes = GetPhenotypes(info[i]);
break;
case PhenotypeIdTag:
phenotypeIds = GetPhenotypeIds(info[i]);
break;
}
}
if (variantType == VariantType.copy_number_gain)
{
observedGains++;
}
if (variantType == VariantType.copy_number_loss)
{
observedLosses++;
}
}
