public override void Write(IEnumerable <CalledAllele> calledAlleles, IRegionMapper mapper = null)
{
var comparer = new AlleleCompareByLociAndAllele();
var sortedVariants = calledAlleles.OrderBy(a => a, comparer);
base.Write(sortedVariants, mapper);
}
public static List <CalledAllele> FilterAndOrderAllelesByFrequency(IEnumerable <CalledAllele> alleles, List <CalledAllele> allelesToPrune,
double minFreqThreshold)
{
var variantAlleles = new List <CalledAllele>();
var comparer = new AlleleCompareByLociAndAllele();
foreach (var allele in alleles)
{
if (allele.Type != AlleleCategory.Reference)
{
if (allele.Frequency >= minFreqThreshold)
{
variantAlleles.Add(allele);
}
else
{
allelesToPrune.Add(allele);
}
}
}
variantAlleles = variantAlleles.OrderByDescending(p => p.Frequency).ThenBy(a => a, comparer).ToList();
//variantAlleles = variantAlleles.OrderByDescending(p => p.Frequency).ToList();
return(variantAlleles);
}
public void DiploidScenariosWithIndels()
{
// what if the frequencies of co-located variants are identical?
//PICS-845 Handling co-located indels
//chr19 3543478 rs763885961 GCC G 45 LowDP DP = 6; GT: GQ: AD: DP: VF: NL: SB: NC./.:0:3,3:6:0.500:20:-100.0000:0.0000
//chr19 3543478 rs752455174 GC G 45 LowDP DP = 6; GT: GQ: AD: DP: VF: NL: SB: NC./.:0:3,3:6:0.500:20:-100.0000:0.0000
var indel1 = TestHelper.CreatePassingVariant(false);
indel1.ReferenceAllele = "GCC";
indel1.AlternateAllele = "G";
indel1.TotalCoverage = 7;
indel1.AlleleSupport = 3;
var indel2 = TestHelper.CreatePassingVariant(false);
indel2.ReferenceAllele = "GC";
indel2.AlternateAllele = "G";
indel2.TotalCoverage = 7;
indel2.AlleleSupport = 3;
var GTC = GetOriginalSettings();
var allelesToPrune = GTC.SetGenotypes(new List <CalledAllele> {
indel1, indel2
});
Assert.Equal(0, allelesToPrune.Count);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, indel1.Genotype);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, indel2.Genotype);
//check order does not matter
allelesToPrune = GTC.SetGenotypes(new List <CalledAllele> {
indel2, indel1
});
Assert.Equal(0, allelesToPrune.Count);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, indel1.Genotype);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, indel2.Genotype);
var comparer = new AlleleCompareByLociAndAllele();
Assert.Equal(1, comparer.Compare(indel1, indel2));
Assert.Equal(-1, comparer.Compare(indel2, indel1));
//lets make double-sure this is deterministic
var SortedList1 = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(
new List <CalledAllele> {
indel1, indel2
}, allelesToPrune, 0.01);
var SortedList2 = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(
new List <CalledAllele> {
indel2, indel1
}, allelesToPrune, 0.01);
Assert.Equal(SortedList1[0], SortedList2[0]);
Assert.Equal(SortedList1[1], SortedList2[1]);
}
public void DiploidScenariosWithMNVs()
{
// what if the frequencies of co-located variants are identical?
//PICS-845 Handling co-located indels (same issue could happen with MNVs, so lets check that)
var mnv1 = TestHelper.CreatePassingVariant(false);
mnv1.ReferenceAllele = "GCC";
mnv1.AlternateAllele = "GAG";
mnv1.TotalCoverage = 7;
mnv1.AlleleSupport = 3;
var mnv2 = TestHelper.CreatePassingVariant(false);
mnv2.ReferenceAllele = "GCC";
mnv2.AlternateAllele = "GCG";
mnv2.TotalCoverage = 7;
mnv2.AlleleSupport = 3;
var GTC = GetOriginalSettings();
var allelesToPrune = GTC.SetGenotypes(new List <CalledAllele> {
mnv1, mnv2
});
Assert.Equal(0, allelesToPrune.Count);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, mnv1.Genotype);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, mnv2.Genotype);
//check order does not matter
allelesToPrune = GTC.SetGenotypes(new List <CalledAllele> {
mnv2, mnv1
});
Assert.Equal(0, allelesToPrune.Count);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, mnv1.Genotype);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, mnv2.Genotype);
var comparer = new AlleleCompareByLociAndAllele();
Assert.Equal(-1, comparer.Compare(mnv1, mnv2));
Assert.Equal(1, comparer.Compare(mnv2, mnv1));
//lets make double-sure this is deterministic
var SortedList1 = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(
new List <CalledAllele> {
mnv1, mnv2
}, allelesToPrune, 0.01);
var SortedList2 = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(
new List <CalledAllele> {
mnv2, mnv1
}, allelesToPrune, 0.01);
Assert.Equal(SortedList1[0], SortedList2[0]);
Assert.Equal(SortedList1[1], SortedList2[1]);
}
