public void OrderVariants()
{
var chr10 = PhasedVariantTestUtilities.CreateDummyVariant("chr10", 123, "A", "C", 1000, 156);
var chrX = PhasedVariantTestUtilities.CreateDummyVariant("chrX", 123, "A", "C", 1000, 156);
var chrXSecond = PhasedVariantTestUtilities.CreateDummyVariant("chrX", 124, "A", "C", 1000, 156);
var chrM = PhasedVariantTestUtilities.CreateDummyVariant("chrM", 123, "A", "C", 1000, 156);
var chrMSecond = PhasedVariantTestUtilities.CreateDummyVariant("chrM", 124, "A", "C", 1000, 156);
var chr9 = PhasedVariantTestUtilities.CreateDummyVariant("chr9", 123, "A", "C", 1000, 156);
var chr9Second = PhasedVariantTestUtilities.CreateDummyVariant("chr9", 124, "A", "C", 1000, 156);
var nonstandardChrZ = PhasedVariantTestUtilities.CreateDummyVariant("chrZ", 123, "A", "C", 1000, 156);
var nonstandardChrA = PhasedVariantTestUtilities.CreateDummyVariant("chrA", 123, "A", "C", 1000, 156);
// ---------------------------------------------------------------------------
// When neither or both is on chrM, shouldn't matter if we set option to prioritize chrM
// ---------------------------------------------------------------------------
// Same chrom, different positions - numeric chrom
Assert.Equal(-1, Extensions.OrderVariants(chr9, chr9Second, true));
Assert.Equal(-1, Extensions.OrderVariants(chr9, chr9Second, false));
Assert.Equal(1, Extensions.OrderVariants(chr9Second, chr9, true));
Assert.Equal(1, Extensions.OrderVariants(chr9Second, chr9, false));
// Same chrom, different positions - chrX
Assert.Equal(-1, Extensions.OrderVariants(chrX, chrXSecond, true));
Assert.Equal(-1, Extensions.OrderVariants(chrX, chrXSecond, false));
Assert.Equal(1, Extensions.OrderVariants(chrXSecond, chrX, true));
Assert.Equal(1, Extensions.OrderVariants(chrXSecond, chrX, false));
// Same chrom, different positions - chrM
Assert.Equal(-1, Extensions.OrderVariants(chrM, chrMSecond, true));
Assert.Equal(-1, Extensions.OrderVariants(chrM, chrMSecond, false));
Assert.Equal(1, Extensions.OrderVariants(chrMSecond, chrM, true));
Assert.Equal(1, Extensions.OrderVariants(chrMSecond, chrM, false));
// Different chroms, one is >=10 (direct string compare would not sort these chroms correctly)
Assert.Equal(-1, Extensions.OrderVariants(chr9, chr10, true));
Assert.Equal(-1, Extensions.OrderVariants(chr9, chr10, false));
// One numeric, one chrX
Assert.Equal(-1, Extensions.OrderVariants(chr9, chrX, true));
Assert.Equal(-1, Extensions.OrderVariants(chr9, chrX, false));
// Same chrom, same position
Assert.Equal(0, Extensions.OrderVariants(chr9, chr9, true));
Assert.Equal(0, Extensions.OrderVariants(chrX, chrX, true));
Assert.Equal(0, Extensions.OrderVariants(chrM, chrM, true));
// ---------------------------------------------------------------------------
// If one is on chrM, option to prioritize chrM matters
// ---------------------------------------------------------------------------
// One numeric, one chrM
Assert.Equal(1, Extensions.OrderVariants(chr9, chrM, true));
Assert.Equal(-1, Extensions.OrderVariants(chr9, chrM, false));
// One chrX, one chrM
Assert.Equal(1, Extensions.OrderVariants(chrX, chrM, true));
Assert.Equal(-1, Extensions.OrderVariants(chrX, chrM, false));
// ---------------------------------------------------------------------------
// Nonstandard chroms should be below numerics and then ordered alphabetically
// ---------------------------------------------------------------------------
// One numeric, one weird
Assert.Equal(-1, Extensions.OrderVariants(chr9, nonstandardChrZ, true));
Assert.Equal(-1, Extensions.OrderVariants(chr9, nonstandardChrZ, false));
// One chrX, one weird
Assert.Equal(-1, Extensions.OrderVariants(chrX, nonstandardChrZ, true));
Assert.Equal(-1, Extensions.OrderVariants(chrX, nonstandardChrZ, false));
// One chrM, one weird
Assert.Equal(-1, Extensions.OrderVariants(chrX, nonstandardChrZ, true));
Assert.Equal(-1, Extensions.OrderVariants(chrX, nonstandardChrZ, false));
// One numeric, one funny
Assert.Equal(-1, Extensions.OrderVariants(chr9, nonstandardChrA, true));
Assert.Equal(-1, Extensions.OrderVariants(chr9, nonstandardChrA, false));
// One chrX, one funny
Assert.Equal(1, Extensions.OrderVariants(chrX, nonstandardChrA, true));
Assert.Equal(1, Extensions.OrderVariants(chrX, nonstandardChrA, false));
// One chrM, one funny
Assert.Equal(1, Extensions.OrderVariants(chrX, nonstandardChrA, true));
Assert.Equal(1, Extensions.OrderVariants(chrX, nonstandardChrA, false));
}
public void Convert()
{
var vcfVar = PhasedVariantTestUtilities.CreateDummyVariant("chr10", 123, "A", "C", 1000, 156);
vcfVar.Genotypes[0]["GT"] = "0/1";
var allele = Extensions.ConvertUnpackedVariant(vcfVar);
Assert.Equal(vcfVar.ReferenceName, allele.Chromosome);
Assert.Equal(vcfVar.VariantAlleles[0], allele.Alternate);
Assert.Equal(vcfVar.ReferenceAllele, allele.Reference);
Assert.Equal(vcfVar.ReferencePosition, allele.Coordinate);
Assert.Equal(new List <FilterType>()
{
}, allele.Filters);
Assert.Equal(Genotype.HeterozygousAltRef, allele.Genotype);
Assert.Equal(AlleleCategory.Snv, allele.Type);
vcfVar.Genotypes[0]["GT"] = "./.";
vcfVar.Filters = "R5x9";
allele = Extensions.ConvertUnpackedVariant(vcfVar);
Assert.Equal(vcfVar.ReferenceName, allele.Chromosome);
Assert.Equal(vcfVar.VariantAlleles[0], allele.Alternate);
Assert.Equal(vcfVar.ReferenceAllele, allele.Reference);
Assert.Equal(vcfVar.ReferencePosition, allele.Coordinate);
Assert.Equal(new List <FilterType>()
{
FilterType.RMxN
}, allele.Filters);
Assert.Equal(Genotype.AltLikeNoCall, allele.Genotype);
Assert.Equal(AlleleCategory.Snv, allele.Type);
vcfVar.Genotypes[0]["GT"] = "1/2";
vcfVar.Filters = "R5x9;SB";
allele = Extensions.ConvertUnpackedVariant(vcfVar);
Assert.Equal(vcfVar.ReferenceName, allele.Chromosome);
Assert.Equal(vcfVar.VariantAlleles[0], allele.Alternate);
Assert.Equal(vcfVar.ReferenceAllele, allele.Reference);
Assert.Equal(vcfVar.ReferencePosition, allele.Coordinate);
Assert.Equal(new List <FilterType>()
{
FilterType.RMxN, FilterType.StrandBias
}, allele.Filters);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, allele.Genotype);
Assert.Equal(AlleleCategory.Snv, allele.Type);
vcfVar.Genotypes[0]["GT"] = "1/1";
vcfVar.Filters = "R8;q30";
allele = Extensions.ConvertUnpackedVariant(vcfVar);
Assert.Equal(vcfVar.ReferenceName, allele.Chromosome);
Assert.Equal(new List <FilterType>()
{
FilterType.IndelRepeatLength, FilterType.LowVariantQscore
}, allele.Filters);
Assert.Equal(Genotype.HomozygousAlt, allele.Genotype);
Assert.Equal(AlleleCategory.Snv, allele.Type);
vcfVar.Genotypes[0]["GT"] = "1/1";
vcfVar.Filters = "lowvariantfreq;multiallelicsite";
allele = Extensions.ConvertUnpackedVariant(vcfVar);
Assert.Equal(vcfVar.ReferenceName, allele.Chromosome);
Assert.Equal(new List <FilterType>()
{
FilterType.LowVariantFrequency, FilterType.MultiAllelicSite
}, allele.Filters);
Assert.Equal(Genotype.HomozygousAlt, allele.Genotype);
Assert.Equal(AlleleCategory.Snv, allele.Type);
}