code: private List<String> calculateTranscriptHgvs(Variant variant, Transcript transcript, String geneId) {
  
          String mutationType = ">";
  
          // Populate HGVSName parse tree.
          HgvsStringBuilder hgvsStringBuilder = new HgvsStringBuilder();
  
          // Populate coordinates.
          // Use cDNA coordinates.
          hgvsStringBuilder.setKind(isCoding(transcript) ? HgvsStringBuilder.Kind.CODING : HgvsStringBuilder.Kind.NON_CODING);
  
          hgvsStringBuilder.setCdnaStart(genomicToCdnaCoord(transcript, variant.getStart()));
          hgvsStringBuilder.setCdnaEnd(hgvsStringBuilder.getCdnaStart());
  
          // Populate prefix.
          hgvsStringBuilder.setTranscriptId(transcript.getId());
          hgvsStringBuilder.setGeneId(geneId);
  
          String reference;
          String alternate;
          // Convert alleles to transcript strand.
          if (transcript.getStrand().equals("-")) {
              reference = String.valueOf(VariantAnnotationUtils.COMPLEMENTARY_NT.get(variant.getReference().charAt(0)));
              alternate = String.valueOf(VariantAnnotationUtils.COMPLEMENTARY_NT.get(variant.getAlternate().charAt(0)));
          } else {
              reference = variant.getReference();
              alternate = variant.getAlternate();
          }
  
          // Populate alleles.
          hgvsStringBuilder.setMutationType(mutationType);
          hgvsStringBuilder.setReference(reference);
          hgvsStringBuilder.setAlternate(alternate);
  
          return Collections.singletonList(hgvsStringBuilder.format());
      }
docs: Generates cdna HGVS names from an SNV.
  @param transcript Transcript object that will be used as a reference