private static MitoHeteroplasmyProvider GetProvider()
{
var provider = new MitoHeteroplasmyProvider();
provider.Add(1, "C", new[] { 0.123, 0.200, 0.301 }, new[] { 1, 3, 4 });
provider.Add(1, "G", new[] { 0.101, 0.201 }, new[] { 1, 2 });
provider.Add(2, "T", new[] { 0, 0.001, 0.002, 0.003 }, new[] { 134, 1111, 936, 203 });
return(provider);
}
public void CapVrf()
{
var provider = new MitoHeteroplasmyProvider();
provider.Add(750, "G", new[] { 0.0, 0.001, 0.002, 0.991, 0.994, 0.995, 0.996, 0.997, 0.998, 0.999 }, new[] { 24, 4, 2, 3, 2, 1, 1, 4, 3, 2460 });
var chrom = ChromosomeUtilities.ChrM;
var position = 750;
var altAlleles = new[] { "G" };
var percentilesSample = provider.GetVrfPercentiles(chrom, position, altAlleles, new[] { 1.0 });
Assert.Single(percentilesSample);
Assert.True(percentilesSample[0].HasValue);
Assert.Equal(1.76, percentilesSample[0].Value, 2);
}
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);
}
