consequenceType.setBiotype(keyValue[1]); break; case "ea_maf":
if (fields.length > 2) { consequenceType.setEnsemblTranscriptId(fields[1]); consequenceType.setBiotype(fields[2]);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags())
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags())
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags()) : null);
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags())
consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype()); consequenceType.setTranscriptAnnotationFlags(transcript.getAnnotationFlags() != null ? new ArrayList<>(transcript.getAnnotationFlags())