capping vrf to 0.999 (#575)

Co-authored-by: Stromberg, Michael <mstromberg@illumina.com>
Illumina · Dec 11, 2020 · 19868c3 · 19868c3
1 parent 78cc3c3
commit 19868c3
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diff --git a/MitoHeteroplasmy/MitoHeteroplasmyProvider.cs b/MitoHeteroplasmy/MitoHeteroplasmyProvider.cs
@@ -52,6 +52,7 @@ public void Add(int position, string altAllele, double[] vrfs, int[] alleleDepth
 
             if (!_alleleToDistribution.TryGetValue(positionAndAltAlleleIntForm, out (double[] Vrfs, double[] Percentiles) data)) return null;
 
+            if (vrf > 0.999) vrf = 0.999;
             return PercentileUtilities.GetPercentile(vrf, data.Vrfs, data.Percentiles);
         }
 

diff --git a/UnitTests/MitoHeteroplasmy/MitoHeteroplasmyProviderTests.cs b/UnitTests/MitoHeteroplasmy/MitoHeteroplasmyProviderTests.cs
@@ -96,5 +96,22 @@ public void GetVrfPercentiles_100()
             Assert.True(percentilesSample[0].HasValue);
             Assert.Equal(100, percentilesSample[0].Value, 2);
         }
+
+        [Fact]
+        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);
+        }
     }
 }