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());
}
