public void EqualityAndHash()
{
var clinGenItem = new ClinGenItem("CGEN101", "chr1", 100, 1000, VariantType.copy_number_gain, 100, 0, ClinicalInterpretation.likely_pathogenic, true, new HashSet <string> {
"phenotype1"
}, new HashSet <string> {
"phenoId1"
});
var clingenHash = new HashSet <ClinGenItem> {
clinGenItem
};
Assert.Equal(1, clingenHash.Count);
Assert.True(clingenHash.Contains(clinGenItem));
}
public IEnumerable <ClinGenItem> GetItems()
{
using (var reader = _reader)
{
string line;
while ((line = reader.ReadLine()) != null)
{
if (IsClinGenHeader(line))
{
continue;
}
var cols = line.OptimizedSplit('\t');
string id = cols[0];
string ucscChrom = cols[1];
if (!_refNameDict.ContainsKey(ucscChrom))
{
continue;
}
var chrom = _refNameDict[ucscChrom];
int start = int.Parse(cols[2]);
int end = int.Parse(cols[3]);
int observedGains = int.Parse(cols[4]);
int observedLosses = int.Parse(cols[5]);
var variantType = GetVariantType(cols[6]);
var clinInterpretation = GetClinInterpretation(cols[7]);
bool validated = cols[8].Equals("True");
var phenotypes = cols[9] == "" ? null : new HashSet <string>(cols[9].OptimizedSplit(','));
var phenotypeIds = cols[10] == "" ? null : new HashSet <string>(cols[10].OptimizedSplit(','));
var currentItem = new ClinGenItem(id, chrom, start, end, variantType, observedGains, observedLosses,
clinInterpretation, validated, phenotypes, phenotypeIds);
yield return(currentItem);
}
}
}
