Fix bug of non coding transcript HGVSc notations (#566)

* Fix bug of non coding transcript HGVSc notations * Remove unnecessary validations * Update transcript model for NR_003085.2 * Mute debugging codes
Illumina · Oct 25, 2020 · 06038b2 · 06038b2
1 parent 47211ec
commit 06038b2
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Showing 4 changed files with 24 additions and 21 deletions.
diff --git a/VariantAnnotation/AnnotatedPositions/Transcript/CdnaSequence.cs b/VariantAnnotation/AnnotatedPositions/Transcript/CdnaSequence.cs
@@ -90,7 +90,7 @@ private void ApplyRnaEdits(StringBuilder sb)
             }
         }
 
-        public int Length => _sequence?.Length ?? _codingRegion.Length;
+        public int Length => _sequence?.Length ?? _codingRegion?.Length ?? 0;
         public Band[] CytogeneticBands => null;
 
         public string Substring(int offset, int length)

diff --git a/VariantAnnotation/Caches/DataStructures/Transcript.cs b/VariantAnnotation/Caches/DataStructures/Transcript.cs
@@ -295,7 +295,7 @@ public static ITranscript Read(BufferedBinaryReader reader,
                 //     rnaEdits, translation);
 
             }
-            
+
             if (id.WithVersion == "NM_175741.1" && sequenceProvider.Assembly != GenomeAssembly.GRCh38)
             {
                 rnaEdits = new IRnaEdit[] 
@@ -304,9 +304,23 @@ public static ITranscript Read(BufferedBinaryReader reader,
                     new RnaEdit(380,380,"C")
                 };
 
-                TranscriptValidator.Validate(sequenceProvider, chromosome, "NM_175741.1", gene.OnReverseStrand,
-                    transcriptRegions,
-                    rnaEdits, translation);
+                // TranscriptValidator.Validate(sequenceProvider, chromosome, "NM_175741.1", gene.OnReverseStrand,
+                //     transcriptRegions,
+                //     rnaEdits, translation);
+
+            }
+
+            if (id.WithVersion == "NR_003085.2" && sequenceProvider.Assembly != GenomeAssembly.GRCh38)
+            {
+                rnaEdits = new IRnaEdit[] 
+                {
+                    new RnaEdit(1703,1703,"G"), 
+                    new RnaEdit(2832,2831,"AAAAAAAAAAAAAAA"),
+                };
+
+                // TranscriptValidator.Validate(sequenceProvider, chromosome, "NR_003085.2", gene.OnReverseStrand,
+                //     transcriptRegions,
+                //     rnaEdits, translation);
 
             }