public void GetVFMultiAllelicTest()
{
string vcf = Path.Combine(TestPaths.LocalTestDataDirectory, "MultiAllelicVariantTest.vcf");
List <RecalibratedVariantsCollection> results = VariantReader.GetVariantFrequencies(vcf);
// First entry is reference; check if added for both SNV and indel
Assert.True(results[0].ContainsKey("chr1:115252175"));
Assert.Equal(4, results[0].Ad[0]);
Assert.True(results[1].ContainsKey("chr1:115252175"));
Assert.Equal(4, results[1].Ad[0]);
// Second entry 1/0 SNV
Assert.Equal(75, results[0].Dp[1]);
Assert.Equal(45, results[0].Ad[1]);
// Third entry 1/1 SNV
Assert.Equal(72, results[0].Ad[2]);
// Fourth entry multiallelic SNV
Assert.True(!results[0].ContainsKey("chr1:115252178"));
// Fifth entry mixed type
Assert.True(!results[0].ContainsKey("chr1:115252179"));
Assert.True(!results[1].ContainsKey("chr1:115252179"));
// Sixth entry multiallelic insertion with 1 major allele
Assert.True(results[1].ContainsKey("chr1:115252180"));
Assert.Equal(37, results[1].Ad[1]);
Assert.Equal(77, results[1].Dp[1]);
}
public void GetVFDeletionTest()
{
string vcf = Path.Combine(TestPaths.LocalTestDataDirectory, "DeletionVariantTest.vcf");
List <RecalibratedVariantsCollection> results = VariantReader.GetVariantFrequencies(vcf);
// First entry should be skipped
Assert.DoesNotContain(115252175, results[0].ReferencePosition);
Assert.DoesNotContain(115252175, results[1].ReferencePosition);
// Second entry 0/. deletion
Assert.Equal(115252176, results[1].ReferencePosition[0]);
Assert.Equal(75, results[1].Dp[0]);
Assert.Equal(45, results[1].Ad[0]);
Assert.DoesNotContain(115252177, results[0].ReferencePosition);
Assert.DoesNotContain(115252177, results[1].ReferencePosition);
// Third entry 0/. deletion with multiallelic interior
Assert.Equal(115252178, results[1].ReferencePosition[1]);
Assert.DoesNotContain(115252179, results[1].ReferencePosition);
Assert.DoesNotContain(115252179, results[0].ReferencePosition);
// Fourth entry 0/. deletion with an interior SNV and an interior insertion
Assert.Equal(115252180, results[1].ReferencePosition[2]);
Assert.Equal(115252181, results[0].ReferencePosition[0]);
Assert.Equal(115252182, results[1].ReferencePosition[3]);
Assert.DoesNotContain(115252183, results[1].ReferencePosition);
Assert.DoesNotContain(115252183, results[0].ReferencePosition);
// Fifth entry is a SNV with an early break from the deletion
Assert.Equal(115254000, results[0].ReferencePosition[1]);
}
public void ReadDiploidVcfTest()
{
string vcf1 = Path.Combine(TestPaths.LocalTestDataDirectory, "diploid1.vcf"); // tests "diploid"
string vcf2 = Path.Combine(TestPaths.LocalTestDataDirectory, "diploid2.vcf"); // tests "Diploid"
string vcf3 = Path.Combine(TestPaths.LocalTestDataDirectory, "diploid3.vcf"); // tests "DIPLOID"
Assert.Throws <VariantReaderException>(() => VariantReader.GetVariantFrequencies(vcf1));
Assert.Throws <VariantReaderException>(() => VariantReader.GetVariantFrequencies(vcf2));
Assert.Throws <VariantReaderException>(() => VariantReader.GetVariantFrequencies(vcf3));
}
public void ReadMinVqTest()
{
string vcf1 = Path.Combine(TestPaths.LocalTestDataDirectory, "minvq1.vcf");
string vcf2 = Path.Combine(TestPaths.LocalTestDataDirectory, "minvq2.vcf");
string vcf3 = Path.Combine(TestPaths.LocalTestDataDirectory, "minvq3.vcf");
Assert.Throws <VariantReaderException>(() => VariantReader.GetVariantFrequencies(vcf1));
Assert.Throws <VariantReaderException>(() => VariantReader.GetVariantFrequencies(vcf2));
var variants = VariantReader.GetVariantFrequencies(vcf3);
Assert.True(variants[1].Count > 0);
}
public void ReadCrushedVcfTest()
{
Assert.Throws <VariantReaderException>(() => VariantReader.GetVariantFrequencies(
Path.Combine(TestPaths.LocalTestDataDirectory, "crushed.vcf")));
}
