break; case "symbol": consequenceType.setGeneName(keyValue[1]); break; default:
throw new InternalError("Transcript '" + name + "' missing in schema field name 'other'"); consequenceType.setGeneName(gene); consequenceType.setEnsemblGeneId(ensGene); consequenceType.setGeneName(""); consequenceType.setEnsemblTranscriptId(""); consequenceType.setSequenceOntologyTerms(Collections.singletonList(sequenceOntologyTerm));
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());
@Override public List<VariantAnnotation> annotate(List<Variant> variants) throws VariantAnnotatorException { if (fail) { throw new VariantAnnotatorException("Fail because reasons"); } return variants.stream().map(v -> { VariantAnnotation a = new VariantAnnotation(); a.setChromosome(v.getChromosome()); a.setStart(v.getStart()); a.setEnd(v.getEnd()); a.setReference(v.getReference()); a.setAlternate(v.getAlternate()); a.setId("an id -- " + key); ConsequenceType ct = new ConsequenceType(); ct.setGeneName("a gene"); ct.setSequenceOntologyTerms(Collections.emptyList()); ct.setExonOverlap(Collections.emptyList()); ct.setTranscriptAnnotationFlags(Collections.emptyList()); a.setConsequenceTypes(Collections.singletonList(ct)); a.setAdditionalAttributes( Collections.singletonMap(GROUP_NAME.key(), new AdditionalAttribute(Collections.singletonMap(VARIANT_ID.key(), v.toString())))); return a; }).collect(Collectors.toList()); }
transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId());