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"))); }