public void ExtractSample_DotInSampleColumn_ReturnEmptySample()
{
var formatIndices = new FormatIndices();
var sample = SampleFieldExtractor.ExtractSample(".", formatIndices, 1, false);
Assert.True(sample.IsEmpty);
}
public void ExtractSample_EmptySampleColumn_ReturnEmptySample()
{
var formatIndices = new FormatIndices();
var sample = SampleFieldExtractor.ExtractSample(null, formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.True(sample.IsEmpty);
}
public void ExtractSample_EmptySampleColumn_ReturnEmptySample()
{
var formatIndices = new FormatIndices();
var sample = SampleFieldExtractor.ExtractSample(null, formatIndices, 1);
Assert.True(sample.IsEmpty);
}
public void ExtractSample_DragenCNV_MCN_LOH(string formatField, string sampleField)
{
var formatIndices = new FormatIndices();
formatIndices.Set(formatField);
var sample = SampleFieldExtractor.ExtractSample(sampleField, formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.True(sample.IsLossOfHeterozygosity);
}
public void ExtractSample_ExpansionHunter()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC");
var sample = SampleFieldExtractor.ExtractSample("1/1:SPANNING/SPANNING:15/15:15-15/15-15:22/22:23/23:0/0:38.270270", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("1/1", sample.Genotype);
Assert.Equal(new[] { 15, 15 }, sample.RepeatUnitCounts);
}
public void ExtractSample_DragenCNV_AsExpected()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:CN:MCN");
var sample = SampleFieldExtractor.ExtractSample("0|1:3:1", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("0|1", sample.Genotype);
Assert.Equal(3, sample.CopyNumber);
Assert.Equal(1, sample.MinorHaplotypeCopyNumber);
}
public void ExtractSample_DragenSomatic_AsExpected()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB:PS");
var sample = SampleFieldExtractor.ExtractSample("0|1:3.96:33,8:0.195:13,6:20,2:41:17,16,4,4:13,20,4,4:534234", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("0|1", sample.Genotype);
Assert.Equal(3.96, sample.SomaticQuality);
Assert.Equal(new[] { 33, 8 }, sample.AlleleDepths);
Assert.Equal(41, sample.TotalDepth);
Assert.Equal(new[] { 8 / 41.0 }, sample.VariantFrequencies);
}
public void ExtractSample_PEPE()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:GQ:AD:DP:VF:NL:SB:NC:US:AQ:LQ");
var sample = SampleFieldExtractor.ExtractSample("0/1:5:338,1:339:0.00295:30:-7.3191:0.0314:0,0,0,1,0,0,17,1,129,21,148,22:3.366:0.000", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("0/1", sample.Genotype);
Assert.Equal(5, sample.GenotypeQuality);
Assert.Equal(new[] { 338, 1 }, sample.AlleleDepths);
Assert.Equal(339, sample.TotalDepth);
Assert.Equal(new[] { 0.00295 }, sample.VariantFrequencies);
Assert.Equal(3.366f, sample.ArtifactAdjustedQualityScore);
Assert.Equal(0.000f, sample.LikelihoodRatioQualityScore);
}
public void ExtractSample_MitoHeteroplasmy_AsExpected()
{
var provider = new MitoHeteroplasmyProvider();
provider.Add(1, "C", new[] { 0.123, 0.200, 0.301 }, new[] { 1, 2, 4 });
provider.Add(1, "G", new[] { 0.101, 0.201 }, new[] { 1, 2 });
var simplePosition = new SimplePosition(ChromosomeUtilities.ChrM, 1, "A", new[] { "C", "T" });
var formatIndices = new FormatIndices();
formatIndices.Set("GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB:PS");
var sample = SampleFieldExtractor.ExtractSample("1|2:3.96:0,15,85:0.195:13,6:20,2:100:17,16,4,4:13,20,4,4:534234", formatIndices, simplePosition, provider);
Assert.Equal(new[] { 15 / 100.0, 85 / 100.0 }, sample.VariantFrequencies);
Assert.Equal(new[] { "14.29", "null" }, sample.HeteroplasmyPercentile);
}
