public void JsonSamplesOutput()
{
using (var reader = new LiteVcfReader(ResourceUtilities.GetReadStream(Resources.InputFiles("Nirvana_unified_json_format.vcf"))))
{
// LP2000021 LP2000022 LP2000023
Assert.Equal("LP2000021", reader.SampleNames[0]);
Assert.Equal("LP2000022", reader.SampleNames[1]);
Assert.Equal("LP2000023", reader.SampleNames[2]);
var variant = VcfUtilities.GetNextVariant(reader, _renamer);
// chr9 138685463 . A C . PASS BaseQRankSum=-1.61165;GQ=120;DP=43;ReadPosRankSum=0;MQ=60;SNVHPOL=3;SNVSB=-65.7;MQRankSum=0 GT:GQX:GQ:DP:DPF:AD 0/0:90:0:31:0:. 0/0:75:0:26:0:. 0/1:161:194:36:0:20,16
// the unified json will call this function to get all the samples and can print them out using GetEntry as shown below
var sampleVariants = variant.ExtractSampleInfo();
Assert.Equal("0/0", sampleVariants[0].Genotype);
Assert.Equal("0/0", sampleVariants[1].Genotype);
Assert.Equal("0/1", sampleVariants[2].Genotype);
const string expectedEntry1 = "{\"totalDepth\":31,\"genotypeQuality\":90,\"genotype\":\"0/0\"}";
const string expectedEntry2 = "{\"totalDepth\":26,\"genotypeQuality\":75,\"genotype\":\"0/0\"}";
const string expectedEntry3 = "{\"variantFreq\":0.4444,\"totalDepth\":36,\"genotypeQuality\":161,\"alleleDepths\":[20,16],\"genotype\":\"0/1\"}";
Assert.Equal(expectedEntry1, sampleVariants[0].ToString());
Assert.Equal(expectedEntry2, sampleVariants[1].ToString());
Assert.Equal(expectedEntry3, sampleVariants[2].ToString());
}
}
public void EmptySamplesTest()
{
using (var reader = new LiteVcfReader(ResourceUtilities.GetReadStream(Resources.InputFiles("Nirvana_unified_json_format.vcf"))))
{
// getting the 4th variant
VcfUtilities.GetNextVariant(reader, _renamer);
VcfUtilities.GetNextVariant(reader, _renamer);
VcfUtilities.GetNextVariant(reader, _renamer);
var variant = VcfUtilities.GetNextVariant(reader, _renamer);
// GT:GQ:GQX:DPI:AD
// 0/1:124:19:5:11,8:PASS:.
// .
// 1/2:55:59:.:0,21:LowGQX:20
// the unified json will call this function to get all the samples and can print them out using GetEntry as shown below
var sampleVariants = variant.ExtractSampleInfo();
var expectedEntry =
"{\"variantFreq\":0.4211,\"genotypeQuality\":124,\"alleleDepths\":[11,8],\"genotype\":\"0/1\"}";
var observedEntry = sampleVariants[0].ToString();
Assert.Equal(expectedEntry, observedEntry);
expectedEntry = "{\"isEmpty\":true}";
observedEntry = sampleVariants[1].ToString();
Assert.Equal(expectedEntry, observedEntry);
expectedEntry =
"{\"variantFreq\":1,\"totalDepth\":20,\"genotypeQuality\":55,\"alleleDepths\":[0,21],\"genotype\":\"1/2\",\"failedFilter\":true}";
observedEntry = sampleVariants[2].ToString();
Assert.Equal(expectedEntry, observedEntry);
}
}
public void MultipleAllelesMultipleSamples()
{
using (var reader = new LiteVcfReader(ResourceUtilities.GetReadStream(Resources.InputFiles("Nirvana_unified_json_format.vcf"))))
{
// LP2000021 LP2000022 LP2000023
Assert.Equal("LP2000021", reader.SampleNames[0]);
Assert.Equal("LP2000022", reader.SampleNames[1]);
Assert.Equal("LP2000023", reader.SampleNames[2]);
// skip the first variant
VcfUtilities.GetNextVariant(reader, _renamer);
var variant = VcfUtilities.GetNextVariant(reader, _renamer);
// GT:GQ:GQX:DPI:AD
// 1/2:46:1:32:0,22,3
// 1/1:147:4:27:0,12,5
// 0/0:365:9:29:0,8,10
// the unified json will call this function to get all the samples and can print them out using GetEntry as shown below
var sampleVariants = variant.ExtractSampleInfo();
Assert.Equal("1/2", sampleVariants[0].Genotype);
Assert.Equal("1/1", sampleVariants[1].Genotype);
Assert.Equal("0/0", sampleVariants[2].Genotype);
// 1/2 - A
var expectedEntry =
"{\"variantFreq\":1,\"totalDepth\":32,\"genotypeQuality\":1,\"alleleDepths\":[0,22,3],\"genotype\":\"1/2\"}";
var observedEntry = sampleVariants[0].ToString();
Assert.Equal(expectedEntry, observedEntry);
// 1/1 - T
expectedEntry = "{\"variantFreq\":1,\"totalDepth\":27,\"genotypeQuality\":4,\"alleleDepths\":[0,12,5],\"genotype\":\"1/1\"}";
observedEntry = sampleVariants[1].ToString();
Assert.Equal(expectedEntry, observedEntry);
// 0/0 - A
expectedEntry = "{\"variantFreq\":1,\"totalDepth\":29,\"genotypeQuality\":9,\"alleleDepths\":[0,8,10],\"genotype\":\"0/0\"}";
observedEntry = sampleVariants[2].ToString();
Assert.Equal(expectedEntry, observedEntry);
}
}
public void SamplesWithFilterAndGq()
{
using (var reader = new LiteVcfReader(ResourceUtilities.GetReadStream(Resources.InputFiles("Nirvana_unified_json_format.vcf"))))
{
// skip the first two variants
VcfUtilities.GetNextVariant(reader, _renamer);
VcfUtilities.GetNextVariant(reader, _renamer);
var variant = VcfUtilities.GetNextVariant(reader, _renamer);
// GT:GQ:DP:DPF:AD:FT:DPI
// 0/1:124:19:5:11,8:PASS:.
// 2/2:58:55:.:0,23:LowGQX:21
// 1/2:55:59:.:0,21:LowGQX:20
// the unified json will call this function to get all the samples and can print them out using GetEntry as shown below
var sampleVariants = variant.ExtractSampleInfo();
Assert.Equal("0/1", sampleVariants[0].Genotype);
Assert.Equal("2/2", sampleVariants[1].Genotype);
Assert.Equal("1/2", sampleVariants[2].Genotype);
var expectedEntry =
"{\"variantFreq\":0.4211,\"genotypeQuality\":124,\"alleleDepths\":[11,8],\"genotype\":\"0/1\"}";
var observedEntry = sampleVariants[0].ToString();
Assert.Equal(expectedEntry, observedEntry);
// 1/1 - T
expectedEntry =
"{\"variantFreq\":1,\"totalDepth\":21,\"genotypeQuality\":58,\"alleleDepths\":[0,23],\"genotype\":\"2/2\",\"failedFilter\":true}";
observedEntry = sampleVariants[1].ToString();
Assert.Equal(expectedEntry, observedEntry);
// 0/0 - A
expectedEntry =
"{\"variantFreq\":1,\"totalDepth\":20,\"genotypeQuality\":55,\"alleleDepths\":[0,21],\"genotype\":\"1/2\",\"failedFilter\":true}";
observedEntry = sampleVariants[2].ToString();
Assert.Equal(expectedEntry, observedEntry);
}
}