addNotNull(transcripts, consequenceType.getEnsemblTranscriptId()); addNotNull(biotype, consequenceType.getBiotype()); addAllNotNull(flags, consequenceType.getTranscriptAnnotationFlags());
putNotNull(ct, CT_TRANSCRIPT_ANNOT_FLAGS, consequenceType.getTranscriptAnnotationFlags()); putNotNull(ct, CT_C_DNA_POSITION_FIELD, consequenceType.getCdnaPosition()); putNotNull(ct, CT_CDS_POSITION_FIELD, consequenceType.getCdsPosition());
if (variant.getAnnotation().getConsequenceTypes() != null) { for (ConsequenceType consequenceType : variant.getAnnotation().getConsequenceTypes()) { if (consequenceType.getTranscriptAnnotationFlags() != null) { flagsInVariant.addAll(consequenceType.getTranscriptAnnotationFlags());