public void ForcedAllele_at_heterozygous_site_get_genotype_others()
{
var calledAllele1 = new CalledAllele(AlleleCategory.Snv)
{
Filters = new List <FilterType> {
FilterType.ForcedReport, FilterType.LowDepth
},
Genotype = Genotype.AltLikeNoCall,
GenotypeQscore = 10
};
var calledAllele2 = new CalledAllele(AlleleCategory.Insertion)
{
Genotype = Genotype.HeterozygousAltRef,
GenotypeQscore = 40
};
var allelesInPos = new List <CalledAllele>
{
calledAllele1,
calledAllele2
};
var processor = new DiploidLocusProcessor();
processor.Process(allelesInPos);
Assert.Equal(40, calledAllele1.GenotypeQscore);
Assert.Equal(Genotype.Others, calledAllele1.Genotype);
}
public void ForceAllele_at_ref_site_get_ref_genotype_and_genotypeQscore()
{
var calledAllele1 = new CalledAllele(AlleleCategory.Snv)
{
Filters = new List <FilterType> {
FilterType.ForcedReport, FilterType.LowDepth
},
Genotype = Genotype.AltLikeNoCall,
GenotypeQscore = 10
};
var calledAllele2 = new CalledAllele(AlleleCategory.Reference)
{
Genotype = Genotype.HomozygousRef,
GenotypeQscore = 100
};
var allelesInPos = new List <CalledAllele>
{
calledAllele1,
calledAllele2
};
var processor = new DiploidLocusProcessor();
processor.Process(allelesInPos);
Assert.Equal(100, calledAllele1.GenotypeQscore);
Assert.Equal(Genotype.HomozygousRef, calledAllele1.Genotype);
}
public void ForceAllele_at_nocall_site_get_genotype_no_call()
{
var calledAllele1 = new CalledAllele(AlleleCategory.Snv)
{
Filters = new List <FilterType> {
FilterType.ForcedReport, FilterType.LowDepth
},
Genotype = Genotype.AltLikeNoCall,
GenotypeQscore = 10
};
var calledAllele2 = new CalledAllele(AlleleCategory.Insertion)
{
Genotype = Genotype.AltLikeNoCall,
GenotypeQscore = 20
};
var allelesInPos = new List <CalledAllele>
{
calledAllele1,
calledAllele2
};
var processor = new DiploidLocusProcessor();
processor.Process(allelesInPos);
Assert.Equal(20, calledAllele1.GenotypeQscore);
Assert.Equal(Genotype.AltLikeNoCall, calledAllele1.Genotype);
}
public void GenotypeQScore_is_the_min_of_nonForced_Allele()
{
var calledAllele1 = new CalledAllele(AlleleCategory.Snv)
{
Filters = new List <FilterType> {
FilterType.ForcedReport, FilterType.LowDepth
},
Genotype = Genotype.AltLikeNoCall,
GenotypeQscore = 10
};
var calledAllele2 = new CalledAllele(AlleleCategory.Insertion)
{
Genotype = Genotype.HeterozygousAlt1Alt2,
GenotypeQscore = 40
};
var calledAllele3 = new CalledAllele(AlleleCategory.Insertion)
{
Genotype = Genotype.HeterozygousAlt1Alt2,
GenotypeQscore = 100
};
var allelesInPos = new List <CalledAllele>
{
calledAllele1,
calledAllele2,
calledAllele3
};
var processor = new DiploidLocusProcessor();
processor.Process(allelesInPos);
Assert.Equal(40, calledAllele1.GenotypeQscore);
Assert.Equal(40, calledAllele2.GenotypeQscore);
Assert.Equal(40, calledAllele3.GenotypeQscore);
Assert.Equal(Genotype.Others, calledAllele1.Genotype);
}