public void Validate_NullReferenceAllele_ThrowException() { SingleVariant variant = GetConfig(); variant.refAllele = null; Assert.Throws <UserErrorException>(() => variant.Validate()); }
public void Validate_ZeroAlternateAlleles_ThrowException() { SingleVariant variant = GetConfig(); variant.altAlleles = new string[0]; Assert.Throws <UserErrorException>(() => variant.Validate()); }
public void Validate_NullPosition_ThrowException() { SingleVariant variant = GetConfig(); variant.position = null; Assert.Throws <UserErrorException>(() => variant.Validate()); }
public void Validate_NullChromosome_ThrowException() { SingleVariant variant = GetConfig(); variant.chromosome = null; Assert.Throws <UserErrorException>(() => variant.Validate()); }
public void Validate_Success() { SingleVariant variant = GetConfig(); Exception ex = Record.Exception(() => { variant.Validate(); }); Assert.Null(ex); }
public void GetVcfFields_AsExpected() { var variant = new SingleVariant { chromosome = "1", position = 100, refAllele = "A", altAlleles = new[] { "C", "AC" }, filters = new[] { "LowGQX", "NoPassedVariantGTs" }, infoField = "SNVHPOL=2;MQ=34", formatField = "GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL:ME:DQ", sampleFields = new[] { "0|0:15:15:6:4:6,0:4,0:2,0:0:PASS:0,18,170:0:.", "0|1:13:0:7:6:6,1:3,0:3,1:0:LowGQX:15,0,147:.:.", "0|1:18:0:9:8:8,1:2,0:6,1:0:LowGQX:20,0,156:.:." }, sampleNames = new[] { "NA12878", "NA12891", "NA12892" } }; string[] vcfFields = variant.GetVcfFields(); Assert.Equal(12, vcfFields.Length); Assert.Equal("1", vcfFields[0]); Assert.Equal("100", vcfFields[1]); Assert.True(vcfFields.SequenceEqual(new[] { "1", "100", ".", "A", "C,AC", ".", "LowGQX;NoPassedVariantGTs", "SNVHPOL=2;MQ=34", "GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL:ME:DQ", "0|0:15:15:6:4:6,0:4,0:2,0:0:PASS:0,18,170:0:.", "0|1:13:0:7:6:6,1:3,0:3,1:0:LowGQX:15,0,147:.:.", "0|1:18:0:9:8:8,1:2,0:6,1:0:LowGQX:20,0,156:.:." })); }
public void Validate_FormatField_NoSampleNamesAndSampleFields_ThrowException() { SingleVariant variant = GetConfig(); variant.formatField = "GT"; Assert.Throws <UserErrorException>(() => variant.Validate()); }
public void Validate_SampleNamesAndSampleFields_NoFormatField_ThrowException() { SingleVariant variant = GetConfig(); variant.sampleNames = new[] { "Bob" }; variant.sampleFields = new[] { "0/1" }; Assert.Throws <UserErrorException>(() => variant.Validate()); }