public void ReadClingenItems()
{
var clingenReader = new ClinGenReader(new FileInfo(Resources.InputFiles("ClinGenMini.tsv")), _renamer);
var clinGenList = clingenReader.ToList();
Assert.Equal("nsv530705", clinGenList[0].Id);
Assert.Equal(564405, clinGenList[0].Start);
Assert.Equal(8597804, clinGenList[0].End);
Assert.Equal(new List <string> {
"Developmental delay AND/OR other significant developmental or morphological phenotypes"
}, clinGenList[0].Phenotypes);
Assert.Equal(new HashSet <string>(), clinGenList[0].PhenotypeIds);
Assert.Equal(ClinicalInterpretation.pathogenic, clinGenList[0].ClinicalInterpretation);
}
public void GetInterval()
{
var clingenReader = new ClinGenReader(new FileInfo(Resources.InputFiles("ClinGenMini.tsv")), _renamer);
var clinGenList = clingenReader.ToList();
var si = clinGenList[0].GetSupplementaryInterval(_renamer);
Assert.Equal("nsv530705", si.StringValues["id"]);
Assert.Equal(564405, si.Start);
Assert.Equal(8597804, si.End);
Assert.Equal(VariantType.copy_number_loss, si.VariantType);
clinGenList[1].MergeItem(clinGenList[2]);
si = clinGenList[1].GetSupplementaryInterval(_renamer);
Assert.Equal("nsv530706", si.StringValues["id"]);
Assert.Equal(564424, si.Start);
Assert.Equal(3262790, si.End);
Assert.Equal(new List <string> {
"HP:0001252", "HP:0001263", "HP:0001627", "HP:0001999", "MedGen:CN001147", "MedGen:CN001157", "MedGen:CN001482", "MedGen:CN001810"
}, si.StringLists["phenotypeIds"]);
}
