addding hgvsg. support for reference variants (#573)

Illumina · Nov 20, 2020 · 2bb5928 · 2bb5928
1 parent e132bcd
commit 2bb5928
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git a/Nirvana/Properties/launchSettings.json b/Nirvana/Properties/launchSettings.json
@@ -166,7 +166,7 @@
     },
     "RR_rnaEdit": {
       "commandName": "Project",
-      "commandLineArgs": " --cache /Users/rroy1/development/Cache/27/GRCh38/Both --ref /Users/rroy1/development/References/7/Homo_sapiens.GRCh38.Nirvana.dat --in Dragen_v3.2-Dragen-Pedigree-RnaEdits-hg38-RefSeq-VEP91.vcf.gz --out rnaEdit",
+      "commandLineArgs": " --cache /Users/rroy1/development/Cache/27/GRCh38/Both --ref /Users/rroy1/development/References/7/Homo_sapiens.GRCh38.Nirvana.dat --in inputs/rnaEdit.vcf --out outputs/rnaEdit",
       "workingDirectory": "/Users/rroy1/development/TestDatasets"
     },
     "RR_chrM": {

diff --git a/UnitTests/VariantAnnotation/AnnotatedPositions/HgvsgNotationTests.cs b/UnitTests/VariantAnnotation/AnnotatedPositions/HgvsgNotationTests.cs
@@ -15,6 +15,7 @@ public sealed class HgvsgNotationTests
 
         [Theory]
         [InlineData(5, 5, "G", "T", VariantType.SNV, "NC_012920.1:g.5G>T")]
+        [InlineData(5, 5, "G", "G", VariantType.SNV, "NC_012920.1:g.5=")]
         [InlineData(5, 7, "GTG", "", VariantType.deletion, "NC_012920.1:g.5_7delGTG")]
         [InlineData(10, 12, "GAC", "", VariantType.deletion, "NC_012920.1:g.12_14delCGA")]
         [InlineData(16, 15, "", "GATA", VariantType.insertion, "NC_012920.1:g.15_16insGATA")]

diff --git a/VariantAnnotation/AnnotatedPositions/HgvsCodingNomenclature.cs b/VariantAnnotation/AnnotatedPositions/HgvsCodingNomenclature.cs
@@ -84,7 +84,7 @@ public static GenomicChange GetGenomicChange(IInterval interval, bool onReverseS
             int altLength = variant.AltAllele.Length;
 
             // sanity check: make sure that the alleles are different
-            if (variant.RefAllele == variant.AltAllele) return GenomicChange.Unknown;
+            if (variant.RefAllele == variant.AltAllele) return GenomicChange.Reference;
 
             // deletion
             if (altLength == 0) return GenomicChange.Deletion;
@@ -118,6 +118,7 @@ public enum GenomicChange
         DelIns,
         Insertion,
         Inversion,
-        Substitution
+        Substitution,
+        Reference
     }
 }
diff --git a/VariantAnnotation/AnnotatedPositions/HgvsUtilities.cs b/VariantAnnotation/AnnotatedPositions/HgvsUtilities.cs
@@ -289,7 +289,9 @@ public static string FormatDnaNotation(string start, string end, string referenc
                 case GenomicChange.Insertion:
                     sb.Append(coordinates + "ins" + alternateBases);
                     break;
-
+                case GenomicChange.Reference:
+                    sb.Append(coordinates + "=");
+                    break;
                 default:
                     throw new InvalidOperationException("Unhandled genomic change found: " + type);
             }